Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1748112 original size:20 final size:20
Alignment explanation
Indices: 1748087--1748195 Score: 152
Period size: 20 Copynumber: 5.5 Consensus size: 20
1748077 CGATTTTCAT
1748087 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* **
1748107 TCGCAACGCGAATTTGGTAAA
1 TCGCAATGCGAA-TACGTAAA
*
1748128 TCGCAATGCGATTACGT--A
1 TCGCAATGCGAATACGTAAA
1748146 TCGCAATGCGAATACGT-AA
1 TCGCAATGCGAATACGTAAA
1748165 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1748185 TCGCAATGCGA
1 TCGCAATGCGA
1748196 TTTACATAGC
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
18 17 0.22
19 18 0.23
20 27 0.35
21 16 0.21
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1748138 original size:59 final size:58
Alignment explanation
Indices: 1748075--1748203 Score: 181
Period size: 58 Copynumber: 2.2 Consensus size: 58
1748065 AAATTCGCGT
* **
1748075 TGCGATTTTCAT-TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGTAAATCGCAA
1 TGCGATTTACATATCGCAATGCGAATACGT-AATCGCAACGCGAA-TACGTAAATCGCAA
* *
1748134 TGCGA-TTACGTATCGCAATGCGAATACGTAATCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACATATCGCAATGCGAATACGTAATCGCAACGCGAATACGTAAATCGCAA
1748191 TGCGATTTACATA
1 TGCGATTTACATA
1748204 GCGCCATTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
57 17 0.27
58 23 0.37
59 22 0.35
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (58 bp):
TGCGATTTACATATCGCAATGCGAATACGTAATCGCAACGCGAATACGTAAATCGCAA
Found at i:1748188 original size:39 final size:41
Alignment explanation
Indices: 1748087--1748200 Score: 155
Period size: 39 Copynumber: 2.9 Consensus size: 41
1748077 CGATTTTCAT
* **
1748087 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGTAAA
*
1748128 TCGCAATGCGATTACGT--ATCGCAATGCGAA-TACGT-AA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGTAAA
*
1748165 TCGCAATGCGAATACGTAAATCGCAATGCGATTTAC
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAC
1748201 ATAGCGCCAT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
37 18 0.28
38 3 0.05
39 24 0.38
40 3 0.05
41 16 0.25
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTACGTAAA
Found at i:1748394 original size:22 final size:22
Alignment explanation
Indices: 1748368--1748430 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
1748358 CGACATCCGT
*
1748368 CCCATCTCCGACGAAATCAGTC
1 CCCATCTCCGACGAAATCAATC
* *
1748390 CCCATCGCCGACGATATCAATC
1 CCCATCTCCGACGAAATCAATC
* *
1748412 TCCATCTCCGGCGAAATCA
1 CCCATCTCCGACGAAATCA
1748431 TTCACGGTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.40, G:0.14, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCAATC
Found at i:1750436 original size:21 final size:21
Alignment explanation
Indices: 1750412--1750455 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1750402 ACGTGAGATT
1750412 GTAGCATCGTTGCAGAATGAG
1 GTAGCATCGTTGCAGAATGAG
1750433 GTAGCATCGTTGCAGAATGAG
1 GTAGCATCGTTGCAGAATGAG
1750454 GT
1 GT
1750456 TCATACTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (21 bp):
GTAGCATCGTTGCAGAATGAG
Found at i:1750742 original size:33 final size:33
Alignment explanation
Indices: 1750683--1750763 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
1750673 ATAGTTTACT
** * * * *
1750683 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAACCGCAACAACAAA
1750717 ATCGCAATGCGAAATGAAAACCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAACCGCAACAACAAA
1750750 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1750764 ATGACTATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 30 0.73
34 11 0.27
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAACCGCAACAACAAA
Found at i:1750874 original size:20 final size:20
Alignment explanation
Indices: 1750846--1750889 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1750836 TCTCTCATTA
*
1750846 CGATGGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
1750866 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
1750886 CGAT
1 CGAT
1750890 TTTAAGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:1750899 original size:20 final size:20
Alignment explanation
Indices: 1750856--1750899 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1750846 CGATGGTCAT
* *
1750856 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
1750876 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
1750896 TTTC
1 TTTC
1750900 AGATTCTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:1751397 original size:21 final size:20
Alignment explanation
Indices: 1751371--1751448 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
1751361 CTCACCTGTC
1751371 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGGCC-CCCCT
*
1751392 ATCGTTTAAGAGG--CCCCT
1 ATCGTTCAAGAGGCCCCCCT
*
1751410 ATCGTCCCTCAAGAGTCCCCTCCT
1 ATCGT---TCAAGAGGCCCC-CCT
*
1751434 ACCGTTCAAGAGGCC
1 ATCGTTCAAGAGGCC
1751449 ACTGTCATCG
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 10 0.22
21 27 0.59
23 2 0.04
24 7 0.15
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCCCCT
Found at i:1752872 original size:14 final size:14
Alignment explanation
Indices: 1752853--1752888 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1752843 ATTGTTTAAT
1752853 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1752867 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1752881 TGATTTGT
1 TGATTTGT
1752889 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1753082 original size:34 final size:33
Alignment explanation
Indices: 1752994--1753087 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
1752984 AAAACAGACT
* **
1752994 ATCGCAACGCGGAAATGACTATCGCAACGAAAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAAAGA
**
1753028 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
*
1753061 ATCTCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
1753088 TGCGAAACTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
Found at i:1753088 original size:20 final size:19
Alignment explanation
Indices: 1753027--1753094 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
1753017 GCAACGAAAG
1753027 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1753046 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
1753060 AATCTCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
1753080 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
1753095 CTAATTTCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
14 7 0.18
16 5 0.13
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1753162 original size:20 final size:20
Alignment explanation
Indices: 1753137--1753230 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
1753127 GCGATTCTCT
1753137 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1753157 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
1753177 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1753197 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1753217 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1753231 AATGAATGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 67 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1755674 original size:24 final size:24
Alignment explanation
Indices: 1755647--1755693 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1755637 CAAAATCCGA
1755647 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1755671 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1755694 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1755702 original size:24 final size:24
Alignment explanation
Indices: 1755651--1755702 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1755641 ATCCGAGTAT
** *
1755651 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1755675 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1755699 TGAC
1 TGAC
1755703 TAGTACTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1756500 original size:20 final size:20
Alignment explanation
Indices: 1756475--1756521 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1756465 AAAATCAGTA
*
1756475 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1756495 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1756515 TTGCGAT
1 TTGCGAT
1756522 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1756531 original size:20 final size:20
Alignment explanation
Indices: 1756508--1756618 Score: 150
Period size: 20 Copynumber: 5.5 Consensus size: 20
1756498 CGATAGTCAG
*
1756508 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1756528 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1756548 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1756568 AATCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
* *
1756589 ATTCGCGTTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
1756609 ATTCGCATTG
1 ATTCGCATTG
1756619 TGAATTAGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 63 0.81
21 15 0.19
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1756539 original size:40 final size:38
Alignment explanation
Indices: 1756495--1756618 Score: 140
Period size: 40 Copynumber: 3.1 Consensus size: 38
1756485 CAGAATCTCG
1756495 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCGCA
* * *
1756535 TTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCGCA
* *
1756575 TTGCGATTTTTCAAATTCGCGTTGCGATTTATGTATTCGCA
1 TTGCGA---TTCAGATTCGCGTTGCGATTTACGTATTCGCA
1756616 TTG
1 TTG
1756619 TGAATTAGGA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 38 0.54
41 27 0.38
43 3 0.04
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (38 bp):
TTGCGATTCAGATTCGCGTTGCGATTTACGTATTCGCA
Found at i:1756644 original size:21 final size:21
Alignment explanation
Indices: 1756620--1756663 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1756610 TTCGCATTGT
1756620 GAATTAGGAAAATCGCAACGC
1 GAATTAGGAAAATCGCAACGC
* * *
1756641 GAATTTGGGAAATCGCAATGC
1 GAATTAGGAAAATCGCAACGC
1756662 GA
1 GA
1756664 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (21 bp):
GAATTAGGAAAATCGCAACGC
Found at i:1757400 original size:2 final size:2
Alignment explanation
Indices: 1757393--1757431 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1757383 GCCATACACC
1757393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1757432 CACACACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1761290 original size:24 final size:24
Alignment explanation
Indices: 1761243--1761290 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1761233 CAAAATTTAA
* * *
1761243 ATTAGTTGAGACTTATAATTTTTT
1 ATTAGTCGAAACTTATAATGTTTT
*
1761267 ATTAGTCGAAACTTATTATGTTTT
1 ATTAGTCGAAACTTATAATGTTTT
1761291 CTAATAATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTAGTCGAAACTTATAATGTTTT
Found at i:1761619 original size:16 final size:17
Alignment explanation
Indices: 1761598--1761643 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1761588 ATATTAAACC
1761598 TTTTT-AGTAATTTAAT
1 TTTTTAAGTAATTTAAT
*
1761614 TTTTTAAGTATTTTAA-
1 TTTTTAAGTAATTTAAT
* *
1761630 TATTTAAATAATTT
1 TTTTTAAGTAATTT
1761644 TATATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTTAAGTAATTTAAT
Found at i:1761685 original size:25 final size:24
Alignment explanation
Indices: 1761635--1761685 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
1761625 TTTAATATTT
**
1761635 AAATAATTTTATATTTAAAAGTTA
1 AAATAATTTTATATTTAAAAAATA
* *
1761659 AAATAAATTTTGTTTTTAAAAAATA
1 AAAT-AATTTTATATTTAAAAAATA
1761684 AA
1 AA
1761686 TAAGTCCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAATAATTTTATATTTAAAAAATA
Found at i:1764946 original size:27 final size:27
Alignment explanation
Indices: 1764909--1764973 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
1764899 GGCTATGAAT
1764909 TTTGTCCCGAATGATCTATGTACTATA
1 TTTGTCCCGAATGATCTATGTACTATA
1764936 TTTGTCCCGAATGATCTATGTACTATA
1 TTTGTCCCGAATGATCTATGTACTATA
1764963 TTTGTCCCGAA
1 TTTGTCCCGAA
1764974 AGACCACTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (27 bp):
TTTGTCCCGAATGATCTATGTACTATA
Found at i:1765676 original size:24 final size:20
Alignment explanation
Indices: 1765619--1765681 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
1765609 TTCCCCTTGA
*
1765619 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
1765639 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
1765662 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
1765682 TATGCATCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 1 0.03
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:1765682 original size:24 final size:22
Alignment explanation
Indices: 1765619--1765683 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
1765609 TTCCCCTTGA
*
1765619 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
1765639 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTTAAC
1765662 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
1765684 TGCATCGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.46
25 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:1768860 original size:14 final size:14
Alignment explanation
Indices: 1768838--1768880 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1768828 CACATCATTC
1768838 ATCATATAAATCAT
1 ATCATATAAATCAT
* *
1768852 ATGATATAATTCAT
1 ATCATATAAATCAT
*
1768866 ATCATA-AAAGCAT
1 ATCATATAAATCAT
1768879 AT
1 AT
1768881 ACTTTACATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (14 bp):
ATCATATAAATCAT
Found at i:1769737 original size:24 final size:20
Alignment explanation
Indices: 1769680--1769757 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
1769670 TTTCCCTTGA
*
1769680 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
1769700 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
1769723 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
1769744 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
1769758 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:1772068 original size:27 final size:27
Alignment explanation
Indices: 1772034--1772085 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1772024 TTTTTTGATT
1772034 TTTAATAA-AATTAAAATTTAATATTTA
1 TTTAATAATAATTAAAATTT-ATATTTA
**
1772061 TTTAATAATTTTTAAAATTTATATT
1 TTTAATAATAATTAAAATTTATATT
1772086 ATTAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAATAATAATTAAAATTTATATTTA
Found at i:1772147 original size:26 final size:27
Alignment explanation
Indices: 1772118--1772176 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
1772108 AGGTGATATT
1772118 TTTTATCTTTTTATT-C-TTTTATTGAA
1 TTTTATCTTTTTATTACATTTTATTG-A
*
1772144 TTTTATTTTTTTATTACATTTTTATTGA
1 TTTTATCTTTTTATTACA-TTTTATTGA
1772172 TTTTA
1 TTTTA
1772177 AAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 14 0.48
27 1 0.03
28 6 0.21
29 8 0.28
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.71
Consensus pattern (27 bp):
TTTTATCTTTTTATTACATTTTATTGA
Found at i:1772422 original size:324 final size:326
Alignment explanation
Indices: 1771493--1772617 Score: 1633
Period size: 324 Copynumber: 3.4 Consensus size: 326
1771483 TAGCTTAATA
* * *
1771493 TTATTTTTTTATTGCA-TTTTATTGATTTTTTTTAAAAAAAATTACTAATAATTTATTTGATCTA
1 TTATTTTTTTATTGCATTTTTATTGA---TTTTTAAAAAAAATAAATAATAATTCATTTGATCTA
* * *
1771557 TCATTTGTAATTAAAAGTTTATTTTAATAATTTTATATTTTTAAACAATTAATATTAAAAGTTAA
63 TCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAA
* * **
1771622 TAAACATTA-TAATTTTTTAAAATATAAAAAAAATATTAAAACAAACTTTTAAA-TAATTTAACA
128 TAAACATTATTAATTTTTTAAAA-ATATAAAAAATATTAAAATAAACTTTTAAATTTTTTTAACA
* * *
1771685 ATAGTTAATAATGTTTATTCATTTTTAATAAAATTAGAATTTAATATTT-TTTTATATTTTTTAA
192 ATAGTTAATAATGTTTATTTATTTTTAATAAAATTAAAATTTAATATTTATTTAATATTTTTTAA
1771749 AATTAATATTATAAATAATATTTTAAATAAAGAGGTGATA-TTTTTAGCTTTATA-T-TTTTATT
257 AATTAATATTATAAATAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTATATTCTTTTATT
1771811 GAATT
322 GAATT
* * * *
1771816 TTAATTTTTTATTGCATTTTTATTGATTTTTTAAAAAAAGTGATTAATAATTCATTTGATCTATC
1 TTATTTTTTTATTGCATTTTTATTGA-TTTTTAAAAAAAATAAATAATAATTCATTTGATCTATC
*
1771881 AATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAACA
65 AATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATA
*
1771946 AACATTATTAATAATTTTTTAAAAATATAAAAAATATTAAAATAAATTTTTAAATTTTTTTAACA
130 AACATTA-T--TAATTTTTTAAAAATATAAAAAATATTAAAATAAACTTTTAAATTTTTTTAACA
* *
1772011 ACAGTTAATAATGTTT-TTTGATTTTTAATAAAATTAAAATTTAATATTTATTTAATAATTTTTA
192 ATAGTTAATAATGTTTATTT-ATTTTTAATAAAATTAAAATTTAATATTTATTTAATATTTTTTA
* * * * * * *
1772075 AAATTTATATTATTAAGAATATTTTATATAAATAGGTGATATTTTTTATCTTTTTATTCTTTTAT
256 AAATTAATATTATAAATAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTATATTCTTTTAT
1772140 TGAATT
321 TGAATT
* *
1772146 TTATTTTTTTATTACATTTTTATTGA-TTTTAAAAAAAATAAATAATAATTCATTTGATTTAT-A
1 TTATTTTTTTATTGCATTTTTATTGATTTTTAAAAAAAATAAATAATAATTCATTTGATCTATCA
*
1772209 ATTGTAATTAAAAGTTTGTTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATAA
66 ATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATAA
* *
1772274 ACATTATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAAATTTTTTTAATAATAG
131 ACATTATTAATTTTTTAAAAATATAAAAAATATTAAAATAAACTTTTAAATTTTTTTAACAATAG
* *
1772339 TTAATAATGTTTATTTATTTTTAATAAAATTATAATTTAATATTTATTTAATATTTTTTTAAATT
196 TTAATAATGTTTATTTATTTTTAATAAAATTAAAATTTAATATTTATTTAATATTTTTTAAAATT
1772404 AATATTATAAATAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTATATTCTCTTTTATTGA
261 AATATTATAAATAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTATA-T-TCTTTTATTGA
1772469 ATTTT
324 A--TT
*
1772474 ATTAAATTTTAATTTTTTATTGTATTTTTATTGATTTTTGAAAAAAAA-AGAATAATAATTCATT
1 -TT--A---T--TTTTTTATTGCATTTTTATTGATTTTT-AAAAAAAATA-AATAATAATTCATT
*
1772538 TGATATATCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAA
56 TGATCTATCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAA
1772603 AAGTCAATAAACATT
121 AAGTCAATAAACATT
1772618 TAAAAAATGT
Statistics
Matches: 722, Mismatches: 52, Indels: 40
0.89 0.06 0.05
Matches are distributed among these distances:
322 103 0.14
323 15 0.02
324 165 0.23
325 33 0.05
326 77 0.11
327 118 0.16
328 46 0.06
329 3 0.00
330 36 0.05
331 1 0.00
334 1 0.00
336 20 0.03
337 5 0.01
338 29 0.04
339 70 0.10
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (326 bp):
TTATTTTTTTATTGCATTTTTATTGATTTTTAAAAAAAATAAATAATAATTCATTTGATCTATCA
ATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATAA
ACATTATTAATTTTTTAAAAATATAAAAAATATTAAAATAAACTTTTAAATTTTTTTAACAATAG
TTAATAATGTTTATTTATTTTTAATAAAATTAAAATTTAATATTTATTTAATATTTTTTAAAATT
AATATTATAAATAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTATATTCTTTTATTGAAT
T
Found at i:1772564 original size:666 final size:632
Alignment explanation
Indices: 1771325--1772617 Score: 1771
Period size: 666 Copynumber: 2.0 Consensus size: 632
1771315 CTTTTAAAAT
* *
1771325 TAATTATTTAAAAATATGAAAAATATTAAAGTAAACTTTTAAAAAAAAGTAACAACAATTAATAA
1 TAATTATTTAAAAATATAAAAAATATTAAAATAAACTTTTAAAAAAAAGTAACAACAATTAATAA
* * * *
1771390 TGTTTATTCATTTTTAATAAAATTAGAATTTTATATTTATTTTATATTTTTTAAAAATTATAAAA
66 TGTTTATTCATTTTTAATAAAATTAAAATTTAATATTTATTTAATAATTTTTAAAAATTATAAAA
* *
1771455 AATATTTTAAATAAAGAGGTGATATTTTTAGCTTAATATTATTTTTTTATTGCATTTTATTGATT
131 AATATTTTAAATAAAGAGGTGATATTTTTAGCTTAATATTATTTTTTAATTGCATTTTATTCATT
* * * *
1771520 TTTTTTAAAAAAAATTACTAATAATTTATTTGATCTATCATTTGTAATTAAAAGTTTATTTTAAT
196 TTTTTTAAAAAAAATAAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAAT
* *
1771585 AATTTTATATTTTTAAACAATTAATATTAAAAGTTAATAAACATTATAATTTTTTAAAATATAAA
261 AATTTTATATTTTTAAACAATTAATATTAAAAGTCAATAAACATTATAATTGTTTAAAATATAAA
1771650 AAAAATATTAAAACAAACTTTTAAATAATTTAACAATAGTTAATAATGTTTATTCATTTTTAATA
326 AAAAATATTAAAACAAACTTTTAAATAATTTAACAATAGTTAATAATGTTTATTCATTTTTAATA
*
1771715 AAATTAGAATTTAATATTTTTTTATATTTTTTAAAATTAATATTATAAATAATATTTTAAATAAA
391 AAATTAGAATTTAATATTTTTTAATATTTTTTAAAATTAATATTATAAATAATATTTTAAATAAA
1771780 GAGGTGATATTTTTAGCTTTATATTTTTATTGAATTTTAATTTTTTATTGCATTTTTATTGATTT
456 GAGGTGATATTTTTAGCTTTATATTTTTATTGAATTTTAATTTTTTATTGCATTTTTATTGATTT
* ** * *
1771845 TTTAAAAAAAGTGATTAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAATATT
521 TTGAAAAAAAAAGAATAATAATTCATTTGATATATCAATTGTAATTAAAAGTTTATTTTAATATT
1771910 TTTATATTTTTAAACAATTAATATTAAAAGTCAACAAACATTATTAA
586 TTTATATTTTTAAACAATTAATATTAAAAGTCAACAAACATTATTAA
* * ****** *
1771957 TAATTTTTTAAAAATATAAAAAATATTAAAATAAATTTTTAAATTTTTTTAACAACAGTTAATAA
1 TAATTATTTAAAAATATAAAAAATATTAAAATAAACTTTTAAAAAAAAGTAACAACAATTAATAA
* * *
1772022 TGTTTTTTGATTTTTAATAAAATTAAAATTTAATATTTATTTAATAATTTTTAAAATTTATATTA
66 TGTTTATTCATTTTTAATAAAATTAAAATTTAATATTTATTTAATAATTTTTAAAAATTATA--A
* * * ** * **
1772087 TTAAGAATATTTTATATAAATAGGTGATATTTTTTATCTTTTTATTCTTTTATTGAATTTTATTT
129 --AA-AATATTTTAAATAAAGAGGTGATA-TTTTTAGCTTAATATTATTTT-TT-AATTGCA---
*
1772152 TTTTATTACATTTTTATTGATTTTAAAAAAAATAAATAATAATTCATTTGATTTAT-AATTGTAA
185 TTTTATT-CA---TT-TT--TTTTAAAAAAAATAAATAATAATTCATTTGATCTATCAATTGTAA
* *
1772216 TTAAAAGTTTGTTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATAAACATTAT
243 TTAAAAGTTTATTTTAATAATTTTATATTTTTAAACAATTAATATTAAAAGTCAATAAACATTA-
* * ** *
1772281 TAATTGTTTAAAA-ATATAAAAAATATTAAAATAAACTTTTAAATTTTTTTAATAATAGTTAATA
307 TAATTGTTTAAAATATAAAAAAAATATTAAAACAAACTTTTAAA-TAATTTAACAATAGTTAATA
* * *
1772345 ATGTTTATTTATTTTTAATAAAATTATAATTTAATATTTATTTAATATTTTTTTAAATTAATATT
371 ATGTTTATTCATTTTTAATAAAATTAGAATTTAATATTT-TTTAATATTTTTTAAAATTAATATT
1772410 ATAAATAATATTTTAAATAAAGAGGTGATATTTTTTAGCTTTATATTCTCTTTTATTGAATTTTA
435 ATAAATAATATTTTAAATAAAGAGGTGATA-TTTTTAGCTTTATA---T-TTTTATTG-------
*
1772475 TTAAATTTTAATTTTTTATTGTATTTTTATTGATTTTTGAAAAAAAAAGAATAATAATTCATTTG
488 ---AATTTTAATTTTTTATTGCATTTTTATTGATTTTTGAAAAAAAAAGAATAATAATTCATTTG
1772540 ATATATCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAA
550 ATATATCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAA
*
1772605 GTCAATAAACATT
615 GTCAACAAACATT
1772618 TAAAAAATGT
Statistics
Matches: 572, Mismatches: 53, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
632 109 0.19
634 1 0.00
636 2 0.00
637 22 0.04
638 17 0.03
639 2 0.00
640 4 0.01
643 7 0.01
644 1 0.00
647 2 0.00
648 2 0.00
649 96 0.17
650 98 0.17
651 53 0.09
652 14 0.02
655 1 0.00
656 8 0.01
666 133 0.23
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (632 bp):
TAATTATTTAAAAATATAAAAAATATTAAAATAAACTTTTAAAAAAAAGTAACAACAATTAATAA
TGTTTATTCATTTTTAATAAAATTAAAATTTAATATTTATTTAATAATTTTTAAAAATTATAAAA
AATATTTTAAATAAAGAGGTGATATTTTTAGCTTAATATTATTTTTTAATTGCATTTTATTCATT
TTTTTTAAAAAAAATAAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAAT
AATTTTATATTTTTAAACAATTAATATTAAAAGTCAATAAACATTATAATTGTTTAAAATATAAA
AAAAATATTAAAACAAACTTTTAAATAATTTAACAATAGTTAATAATGTTTATTCATTTTTAATA
AAATTAGAATTTAATATTTTTTAATATTTTTTAAAATTAATATTATAAATAATATTTTAAATAAA
GAGGTGATATTTTTAGCTTTATATTTTTATTGAATTTTAATTTTTTATTGCATTTTTATTGATTT
TTGAAAAAAAAAGAATAATAATTCATTTGATATATCAATTGTAATTAAAAGTTTATTTTAATATT
TTTATATTTTTAAACAATTAATATTAAAAGTCAACAAACATTATTAA
Found at i:1773549 original size:306 final size:312
Alignment explanation
Indices: 1772977--1773717 Score: 1063
Period size: 306 Copynumber: 2.3 Consensus size: 312
1772967 TCGCGGTCAG
*
1772977 TAAAAATGATGAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAATAATTT
1 TAAAAATG-TGAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAATATTTT
1773042 TATATTTTTAAACAATTAATATTAAAAGTCGACA-AACATTATTAATTGTTTAAAAATATAAAAA
65 TATATTTTTAAACAATTAATATTAAAAGTC-A-ATAACATTATTAATTGTTTAAAAATATAAAAA
*
1773106 ATATTAAAACAAACTTTTAAATTTTTTTAACAACAATTAATAATGTTTATTCATTTTTAATAAAT
128 ATATTAAAACAAACTTTTAAATTTTTTTAACAACAATTAATAATATTTATTCATTTTTAATAAAT
* *
1773171 TAGAATTTAATATTTATTTTATAGTTTTTAAAATTAATATTATAATGAATATTTTAAATAAATAG
193 TAAAATTTAATATTTATTTTATAGTTTTTAAAATTAATATTATAATGAATATTTTAAATAAAGAG
*
1773236 GTGATATTTTTTAGCTTTATA-TTATTTATT-A-CA-TTTTTATTG-ATTTTT-T
258 ATGATATTTTTTAGCTTTATATTTATTTATTAATCATTTTTTATTGTATTTTTAT
* * *
1773285 TAAAAATGTGAATAATAATTCATTTAATCTATTAATTGTAATTAAAAGTTTGTTTTAATATTTTT
1 TAAAAATGTGAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAATATTTTT
*
1773350 ATATTTTTAAACAATTAATATTAAAAGTCAATAACTTTATTAATTGTTTAAAAATATAAAAAATA
66 ATATTTTTAAACAATTAATATTAAAAGTCAATAACATTATTAATTGTTTAAAAATATAAAAAATA
* * * *
1773415 TTAAAATAAACTTTTAAATTTTTTTAACAACAGTTAATAATATTTGTTTATTTTTAATAAAATTA
131 TTAAAACAAACTTTTAAATTTTTTTAACAACAATTAATAATATTTATTCATTTTTAAT-AAATTA
1773480 AAATTTAATATTTATTTTATA-TTTTTAAAATTAATATTATAAAT-AATATTTTAAATAAAGAGA
195 AAATTTAATATTTATTTTATAGTTTTTAAAATTAATATTAT-AATGAATATTTTAAATAAAGAGA
* *
1773543 TGATATTTTTTAGCTTTATATTCTTTTTTTTATTGAATTTTATTTTTTTATTGTATTTTTAT
259 TGATATTTTTTAGCTTTATA----TTTATTTATT-AA--TCA-TTTTTTATTGTATTTTTAT
* * *
1773605 TATTTTTGAAAAAGTGAATAATAATTCATTTGATATATCAATTGTAATTAAAAATTTATTTTAA-
1 TA------AAAATGTGAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAAT
1773669 ATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATAAACATT-TTAA
60 ATTTTTATATTTTTAAACAATTAATATTAAAAGTCAAT-AACATTATTAA
1773718 AAAATATCAC
Statistics
Matches: 387, Mismatches: 22, Indels: 31
0.88 0.05 0.07
Matches are distributed among these distances:
305 1 0.00
306 142 0.37
307 111 0.29
308 8 0.02
311 8 0.02
313 1 0.00
316 1 0.00
318 9 0.02
319 6 0.02
320 3 0.01
325 42 0.11
326 55 0.14
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (312 bp):
TAAAAATGTGAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTTTATTTTAATATTTTT
ATATTTTTAAACAATTAATATTAAAAGTCAATAACATTATTAATTGTTTAAAAATATAAAAAATA
TTAAAACAAACTTTTAAATTTTTTTAACAACAATTAATAATATTTATTCATTTTTAATAAATTAA
AATTTAATATTTATTTTATAGTTTTTAAAATTAATATTATAATGAATATTTTAAATAAAGAGATG
ATATTTTTTAGCTTTATATTTATTTATTAATCATTTTTTATTGTATTTTTAT
Found at i:1773588 original size:18 final size:19
Alignment explanation
Indices: 1773567--1773611 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1773557 TTTATATTCT
1773567 TTTTTTTATTG-AATTTTA
1 TTTTTTTATTGTAATTTTA
*
1773585 TTTTTTTATTGTATTTTTA
1 TTTTTTTATTGTAATTTTA
1773604 TTATTTTT
1 TT-TTTTT
1773612 GAAAAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.46
19 8 0.33
20 5 0.21
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTTTATTGTAATTTTA
Found at i:1773955 original size:18 final size:19
Alignment explanation
Indices: 1773929--1773970 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1773919 CAAAAAGTGT
*
1773929 TAAATTGATAAAT-AAAGA
1 TAAAATGATAAATGAAAGA
* *
1773947 TAAAATGATATATGACAGA
1 TAAAATGATAAATGAAAGA
1773966 TAAAA
1 TAAAA
1773971 AAAAATTGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (19 bp):
TAAAATGATAAATGAAAGA
Found at i:1786197 original size:31 final size:31
Alignment explanation
Indices: 1786159--1786312 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
1786149 CCCGAAGGAC
* *
1786159 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1786190 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1786221 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1786252 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1786283 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1786313 CCCTCGACCC
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1787018 original size:21 final size:21
Alignment explanation
Indices: 1786988--1787032 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1786978 ATTCTGTCGT
*
1786988 TTGAAGGGGTATC-GGTTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
*
1787009 TTGAATGGGTACAGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
1787030 TTG
1 TTG
1787033 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:1795428 original size:37 final size:37
Alignment explanation
Indices: 1795386--1795512 Score: 119
Period size: 37 Copynumber: 3.6 Consensus size: 37
1795376 TTTTGAAAAA
1795386 AAATAATAA-CTAAGTGACCAAATAGGTAGTTTAACCT
1 AAATAATAATC-AAGTGACCAAATAGGTAGTTTAACCT
* * *
1795423 AAATAATAATCGAGTGACCTAAACA--TA----AA-TT
1 AAATAATAATCAAGTGACC-AAATAGGTAGTTTAACCT
* *
1795454 AGATAATATAT-AAGTGACCAAATAGGTAGTTTACCCT
1 AAATAATA-ATCAAGTGACCAAATAGGTAGTTTAACCT
1795491 AAATAATAATCAAGTGACCAAA
1 AAATAATAATCAAGTGACCAAA
1795513 ACATAAATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
30 4 0.06
31 15 0.21
32 6 0.09
36 5 0.07
37 35 0.50
38 5 0.07
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (37 bp):
AAATAATAATCAAGTGACCAAATAGGTAGTTTAACCT
Found at i:1795470 original size:31 final size:31
Alignment explanation
Indices: 1795435--1795543 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 31
1795425 ATAATAATCG
*
1795435 AGTGACCTAAACATAAATTAGATAATATATA
1 AGTGACCTAAACATAAATTACATAATATATA
* ** *
1795466 AGTGACC-AAATAGGTAGTTTACCCTAAATAATAATCA
1 AGTGACCTAAACA--TAAATTA-CAT-AAT-AT-AT-A
* *
1795503 AGTGACCAAAACATAAATTATATAATATATA
1 AGTGACCTAAACATAAATTACATAATATATA
1795534 AGTGA-CTAAA
1 AGTGACCTAAA
1795544 TAGGTAGTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 17
0.68 0.13 0.20
Matches are distributed among these distances:
30 8 0.14
31 13 0.22
32 7 0.12
33 3 0.05
34 6 0.10
35 3 0.05
36 7 0.12
37 8 0.14
38 4 0.07
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.28
Consensus pattern (31 bp):
AGTGACCTAAACATAAATTACATAATATATA
Found at i:1795497 original size:68 final size:68
Alignment explanation
Indices: 1795386--1795629 Score: 366
Period size: 68 Copynumber: 3.6 Consensus size: 68
1795376 TTTTGAAAAA
*
1795386 AAATAATA-ACTAAGTGACCAAATAGGTAGTTTAACCTAAATAATAATCGAGTGACCTAAACATA
1 AAATAATATA-TAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCTAAACATA
1795450 AATT
65 AATT
* * *
1795454 AGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCAAGTGACCAAAACATAA
1 AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCTAAACATAA
1795519 ATT
66 ATT
* * * *
1795522 ATATAATATATAAGTGACTAAATAGGTAGTTTACCCTAAATAAAAATTGAGTGA-CTAAAACATA
1 AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCT-AAACATA
1795586 AATT
65 AATT
* *
1795590 AAATAATATATAAGTGACCAAATATGTAGTTTATCCTAAA
1 AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAA
1795630 AAACTTCCCT
Statistics
Matches: 160, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
67 1 0.01
68 158 0.99
69 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.29
Consensus pattern (68 bp):
AAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGACCTAAACATAA
ATT
Found at i:1795606 original size:31 final size:31
Alignment explanation
Indices: 1795490--1795607 Score: 78
Period size: 31 Copynumber: 3.6 Consensus size: 31
1795480 TAGTTTACCC
*
1795490 TAAATAATA-ATCAAGTGACCAAAACATAAAT
1 TAAATAATATAT-AAGTGACTAAAACATAAAT
* * ***
1795521 TATATAATATATAAGTGACTAAATAGGTAGTTTACCC
1 TAAATAATATATAAGTGACTAAA-A--CA---TAAAT
* *
1795558 TAAATAA-AAATTGAGTGACTAAAACATAAAT
1 TAAATAATATA-TAAGTGACTAAAACATAAAT
1795589 TAAATAATATATAAGTGAC
1 TAAATAATATATAAGTGAC
1795608 CAAATATGTA
Statistics
Matches: 63, Mismatches: 15, Indels: 18
0.66 0.16 0.19
Matches are distributed among these distances:
31 34 0.54
32 5 0.08
34 2 0.03
36 3 0.05
37 19 0.30
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (31 bp):
TAAATAATATATAAGTGACTAAAACATAAAT
Found at i:1804031 original size:13 final size:13
Alignment explanation
Indices: 1804013--1804037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1804003 TGAGATATTT
1804013 ATTTTTATAATTA
1 ATTTTTATAATTA
1804026 ATTTTTATAATT
1 ATTTTTATAATT
1804038 TATATCTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTATAATTA
Found at i:1804450 original size:20 final size:19
Alignment explanation
Indices: 1804412--1804455 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1804402 CTGAAAATTC
1804412 TCATTAAAAAAGTTTAAAT
1 TCATTAAAAAAGTTTAAAT
*
1804431 GTCATTTAAAAA-TTTAAAAT
1 -TCATTAAAAAAGTTT-AAAT
1804451 TCATT
1 TCATT
1804456 GTTCATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (19 bp):
TCATTAAAAAAGTTTAAAT
Found at i:1804455 original size:19 final size:20
Alignment explanation
Indices: 1804412--1804448 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1804402 CTGAAAATTC
1804412 TCATTAAAAAAGTTTAAATG
1 TCATTAAAAAAGTTTAAATG
*
1804432 TCATTTAAAAA-TTTAAA
1 TCATTAAAAAAGTTTAAA
1804449 ATTCATTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TCATTAAAAAAGTTTAAATG
Found at i:1804586 original size:19 final size:18
Alignment explanation
Indices: 1804544--1804587 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1804534 TACATTTATT
* *
1804544 GTATTTTTAGTAGTATAG
1 GTATTTTTAATAATATAG
1804562 GATATTTTTAATAATATGAG
1 G-TATTTTTAATAATAT-AG
1804582 GTATTT
1 GTATTT
1804588 ACAAGGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
GTATTTTTAATAATATAG
Found at i:1811666 original size:41 final size:41
Alignment explanation
Indices: 1811609--1811729 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
1811599 AATGACCAAC
* *
1811609 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTG
1 AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
* *
1811650 AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
1 AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
*
1811691 AAAATCGCATTGCGATTTTTCATTTCGCGTTGCGATAGT
1 AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGT
1811730 CTACAGTTGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (41 bp):
AAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
Found at i:1811679 original size:20 final size:20
Alignment explanation
Indices: 1811619--1811726 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
1811609 AAAATCGCAA
1811619 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* * ** **
1811639 TGAGATAGTTGAAAATCGCGT
1 TGCGAT-TTTCCATTTCGCGT
1811660 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** *
1811680 TGCGATAGTTT-AAAATCGCAT
1 TGCGAT--TTTCCATTTCGCGT
*
1811701 TGCGATTTTTCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
1811721 TGCGAT
1 TGCGAT
1811727 AGTCTACAGT
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
19 3 0.05
20 32 0.50
21 26 0.41
22 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:1811752 original size:41 final size:40
Alignment explanation
Indices: 1811609--1811775 Score: 185
Period size: 41 Copynumber: 4.1 Consensus size: 40
1811599 AATGACCAAC
** *
1811609 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTT
1 AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
1811649 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTT
1 -AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG-TT
* *
1811691 AAAATCGCATTGCGATTTTTCATTTCGCGTTGCGATAGTCT
1 AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-T
* * * * *
1811732 ACAGTTGTCGTTGCGATTTTCCAAATT--CGTTGTGATAGTT
1 AAAATCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTT
1811772 AAAA
1 AAAA
1811776 AAAAAGATTT
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
40 4 0.04
41 87 0.81
42 14 0.13
43 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (40 bp):
AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
Found at i:1811763 original size:82 final size:81
Alignment explanation
Indices: 1811609--1811776 Score: 205
Period size: 82 Copynumber: 2.0 Consensus size: 81
1811599 AATGACCAAC
*
1811609 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
*
1811674 TCGCGTTGCGATAGTTT
66 TC-CGTTGCGATAGTTA
* * * * * *
1811691 AAAATCGCATTGCGATTTTTCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCA
1 AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGT-TGAAAATCG-CGTTGCGATTTTCC-
*
1811755 AATT-CGTTGTGATAGTTA
63 AATTCCGTTGCGATAGTTA
1811773 AAAA
1 AAAA
1811777 AAAAGATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 56 0.76
83 15 0.20
84 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (81 bp):
AAAATCGCAATGCGATTTTCCATTTCGCGTTGAGATAGTTGAAAATCGCGTTGCGATTTTCCAAT
TCCGTTGCGATAGTTA
Found at i:1812374 original size:6 final size:6
Alignment explanation
Indices: 1812365--1812418 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
1812355 CGTCGTCTCG
1812365 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1812413 GGTCGT
1 GGTCGT
1812419 ACGTGTCTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1812570 original size:41 final size:41
Alignment explanation
Indices: 1812500--1812796 Score: 346
Period size: 41 Copynumber: 7.0 Consensus size: 41
1812490 TCAACGAATT
* *
1812500 TGGAAAATCGCAACGAC-AACTGCAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGAATTTCA-ACTATCGCAACGCGAAA
**
1812542 TGGAAAATCGCAATTCGAATTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
*
1812583 TGGAAAATCGCAACGCGAATTTCAACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
*
1812624 TGGAAAATCGCAACGCGAATTTCAACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
* * *
1812665 TGGAAAATCGCAACGCGATTTTCAACTATCGTAACGCGAATT
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAA-A
* * * *
1812707 TGCAATAGT-GGAGATCGCGTTGCGATTTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCA-A-CGC---G-AATTTCAACTATCGCAACGCGAAA
* * *
1812754 TGGAAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
1812795 TG
1 TG
1812797 CAACGTGAAT
Statistics
Matches: 220, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
41 157 0.71
42 25 0.11
43 3 0.01
44 3 0.01
45 3 0.01
46 2 0.01
47 7 0.03
48 20 0.09
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
Found at i:1812574 original size:21 final size:21
Alignment explanation
Indices: 1812525--1812707 Score: 140
Period size: 20 Copynumber: 8.9 Consensus size: 21
1812515 ACAACTGCAG
* **
1812525 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* **
1812546 A-AATCGCAATTCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* **
1812566 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
*
1812587 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* * **
1812607 ACTATCGCAATGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
*
1812628 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* * **
1812648 ACTATCGCAATGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
1812669 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
*
1812689 ACTATCGTAACGCGAATTT
1 ACTATCGCAACGCGAATTT
1812708 GCAATAGTGG
Statistics
Matches: 118, Mismatches: 40, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
20 59 0.50
21 59 0.50
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTCA
Found at i:1812751 original size:20 final size:20
Alignment explanation
Indices: 1812728--1812792 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1812718 AGATCGCGTT
1812728 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** * *
1812748 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTTCAACTATCGCAAC
*
1812768 GCGATTTTCAACTATCGCAAT
1 GCGA-TTTCAACTATCGCAAC
1812789 GCGA
1 GCGA
1812793 AATGCAACGT
Statistics
Matches: 31, Mismatches: 11, Indels: 5
0.66 0.23 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 14 0.45
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:1812800 original size:21 final size:21
Alignment explanation
Indices: 1812735--1812800 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1812725 GTTGCGATTT
1812735 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
1812756 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
1812776 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1812797 CAAC
1 CAAC
1812801 GTGAATTTGC
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1812982 original size:21 final size:23
Alignment explanation
Indices: 1812940--1812992 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
1812930 ATTTTCTCTA
*
1812940 AATTTTAATATTAAAATCAA-TT
1 AATTTAAATATTAAAATCAATTT
1812962 AATTTAAAT-TTAAATAT-AATTT
1 AATTTAAATATTAAA-ATCAATTT
1812984 AATTATAAA
1 AATT-TAAA
1812993 ATAAAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 16 0.59
23 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAAATATTAAAATCAATTT
Found at i:1814571 original size:34 final size:34
Alignment explanation
Indices: 1814512--1814578 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1814502 TTCTTGAGAG
*
1814512 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTCA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTCA
1814546 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
1814579 AATTCATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTCA
Found at i:1816035 original size:4 final size:4
Alignment explanation
Indices: 1816026--1816061 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
1816016 AACAGCATGT
1816026 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1816062 AAAGAGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:1824895 original size:54 final size:55
Alignment explanation
Indices: 1824830--1825026 Score: 220
Period size: 54 Copynumber: 3.6 Consensus size: 55
1824820 GCTACAGCTG
*
1824830 GATGAATGTATTGTCAAATGTTTTACAAACATATGGGCAGAAGCCACA-GAAAAT
1 GATGAATGTATTGTCAAATGTTTTACAAACATCTGGGCAGAAGCCACAGGAAAAT
* * * * * * * * *
1824884 GATGAATGTATTATCAGATGTTTTACTAGCATCTGAGAAGAAACCACATG-AGAT
1 GATGAATGTATTGTCAAATGTTTTACAAACATCTGGGCAGAAGCCACAGGAAAAT
* * **
1824938 GATGAATGTGTTGTCAAATATTTTATGAACATCTGGGCAGAAGCCACAGGAAAA-
1 GATGAATGTATTGTCAAATGTTTTACAAACATCTGGGCAGAAGCCACAGGAAAAT
* *
1824992 GATGAATGTGTTGCCAAATGTTTTACGAAACATCT
1 GATGAATGTATTGTCAAATGTTTTAC-AAACATCT
1825027 ATACATAAGT
Statistics
Matches: 115, Mismatches: 25, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
54 105 0.91
55 10 0.09
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (55 bp):
GATGAATGTATTGTCAAATGTTTTACAAACATCTGGGCAGAAGCCACAGGAAAAT
Found at i:1826011 original size:102 final size:103
Alignment explanation
Indices: 1825831--1826027 Score: 297
Period size: 102 Copynumber: 1.9 Consensus size: 103
1825821 ATTCGATGGG
* *
1825831 TCAACTTTTCCAGATAAAGTTCATAATGAGACGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
1 TCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
*
1825896 TGAGAATAACTTGTTCAA-CTTTAGCTTGATCGACGGA
66 TGAGAAGAACTTGTTCAACCTTTAGCTTGATCGACGGA
* * * * *
1825933 TCAACATTTCCATATAGAGTTCATAATGGGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
1 TCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
* *
1825998 TGAGAAGAGCTTGTTCAACCTTTTGCTTGA
66 TGAGAAGAACTTGTTCAACCTTTAGCTTGA
1826028 CTCCATTTCC
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 74 0.88
103 10 0.12
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (103 bp):
TCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTAGCTTGATCGACGGA
Found at i:1826259 original size:113 final size:112
Alignment explanation
Indices: 1826061--1826728 Score: 495
Period size: 113 Copynumber: 5.7 Consensus size: 112
1826051 GCACCAGAGC
*
1826061 CATTGCCAGGTAGAGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
1 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
* * * *
1826126 AATAACTTGTTCAACCTTTTGCTCGAATTCATCATTCGATGGATCAG
66 AAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCCATGGATCAA
1826173 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGA
*
1826238 GAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTCCATGGATCAA
65 GAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCCATGGATCAA
* * * *
1826286 CATTGCCAGAG-AAAGTTCATAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATGA
1 CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
* * ***
1826350 GAAGAACTGGTTCAACC-TTTGCAT-G-ACTCTATCACAGAATGAGATAAATCAACACCGA
65 GAAGAACTTGTTCAACCTTTTGC-TCGAATTC-ATCACTCCATG-G----AT---CA---A
* *
1826408 CATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCT------GAAGAAGAAGTTCATAATGA
1 CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
* *** *
1826466 GAAGAACTTGTTCAACC-TTTGCTTG-ATTCTATCACAGAAAGAGATAGATCATCA
65 GAAGAACTTGTTCAACCTTTTGCTCGAATTC-ATCAC-----TCCATGGATCA--A
* ** * *
1826520 TCAACTTTTCCA-AAAGAGTTCATAATGAGAAGAACTCATCCGAAGAAGG-AGAATAAGTTCATA
1 -C-A--TTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATA
* ** * ** * *
1826583 ATAAGAAGAACTTGTTCAACCTTTTGCTCGGCTTTATCACAGAAGGAGATAGATCAGCACCAA
61 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCAC---------TCCAT--GGATCAA
* * * *
1826646 CATTTCCAGAG-AAAGTTCATAATGAGAAAAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGA
1 CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
*
1826710 GAAAAACTTGTTCAACCTT
65 GAAGAACTTGTTCAACCTT
1826729 GCCTTAATTC
Statistics
Matches: 462, Mismatches: 50, Indels: 77
0.78 0.08 0.13
Matches are distributed among these distances:
110 3 0.01
111 14 0.03
112 80 0.17
113 105 0.23
114 2 0.00
115 26 0.06
116 60 0.13
119 2 0.00
120 1 0.00
121 35 0.08
122 58 0.13
123 63 0.14
124 1 0.00
125 1 0.00
126 8 0.02
128 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (112 bp):
CATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCCATGGATCAA
Found at i:1826430 original size:122 final size:121
Alignment explanation
Indices: 1826283--1826728 Score: 568
Period size: 122 Copynumber: 3.7 Consensus size: 121
1826273 CTCCATGGAT
* * *
1826283 CAACATTGCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
* * *
1826348 GAGAAGAACTGGTTCAACCTTTGCATGACTCTATCACAGAATGAGATAAATCAACAC
66 GAGAAGAACTTGTTCAACCTTTGC-TGACTCTATCACAGAAAGAGATAGATCAACAC
*
1826405 CGACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT-----G-AAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
* * *
1826464 GAGAAGAACTTGTTCAACCTTTGCTTGATTCTATCACAGAAAGAGATAGATCATCAT
66 GAGAAGAACTTGTTCAACCTTTGC-TGACTCTATCACAGAAAGAGATAGATCAACAC
* * * *
1826521 CAACTTTTCCA-A-AAGAGTTCATAATGAGAAGAACTCATCCGAAGA-AGGAGAATAAGTTCATA
1 CAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAGA-AAGAAGAAGTTCATA
* * * * *
1826583 ATAAGAAGAACTTGTTCAACCTTTTGCTCGGCTTTATCACAGAAGGAGATAGATCAGCAC
64 ATGAGAAGAACTTGTTCAACC-TTTGCT-GACTCTATCACAGAAAGAGATAGATCAACAC
* * *
1826643 CAACATTTCCAGAGAAAGTTCATAATGAGAAAAACTCATCTGAAAAGGAAGAAGAAGTTCATAAT
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
*
1826708 GAGAAAAACTTGTTCAACCTT
66 GAGAAGAACTTGTTCAACCTT
1826729 GCCTTAATTC
Statistics
Matches: 279, Mismatches: 32, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
114 2 0.01
115 25 0.09
116 76 0.27
117 1 0.00
121 34 0.12
122 79 0.28
123 60 0.22
124 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (121 bp):
CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAGAAGAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTGCTGACTCTATCACAGAAAGAGATAGATCAACAC
Found at i:1826468 original size:17 final size:17
Alignment explanation
Indices: 1826420--1826471 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1826410 TTTCCAGAGA
1826420 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
* *
1826437 AA-CTCAT-CTGAAGAAG
1 AAGTTCATAATG-AGAAG
1826453 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
1826470 AA
1 AA
1826472 CTTGTTCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.21
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:1826580 original size:349 final size:337
Alignment explanation
Indices: 1825831--1826612 Score: 845
Period size: 349 Copynumber: 2.3 Consensus size: 337
1825821 ATTCGATGGG
* *
1825831 TCAACTTTTCCAGATAA-AGTTCATAATGAGACGAACTCATCTGAAG-AGAAAGAAGAAGTTCAT
1 TCAACTTTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-GAGAAGAAGTTCAT
* * * * * * * *
1825894 AATGAGAATAACTTGTTCAA-CTTTAGCTTGATCGACGGATCAACATTTCCATATAGAGTTCATA
64 AATGAGAAGAACTTGTTCAACCTTTTGCTCGATCCACGGATCAACATTGCCAGAGAAAGTTCATA
** * * *
1825958 ATGGGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTG
129 ATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTGGTTCAACCTTTTG
* * * * * * *
1826023 CTTGACTCCATTTCCAGAAAGAGATAGAGCACCAGAGCCATTGCCAGGTAGAGTTCATAATGAGA
194 CATGACTCCATATCCAGAAAGAGATAAAGCAACACAGACATTGCCAGGTAAAGTTCATAATGAGA
*
1826088 AAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTTTGCTCGAA
259 AAAACTCATCT----A-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAA
*** *
1826153 TTCATCATTCGATGGATCA
319 TTCATCAAGAGATGCATCA
* * **
1826172 GC-A--TTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 TCAACTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATA
*
1826234 ATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTCCATGGATCAACATTGCCAGAGAA
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCG-A-TC--CA---C--GGATCAACATTGCCAGAGAA
1826299 AGTTCATAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTGGTTCA
121 AGTTCATAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTGGTTCA
* * * *
1826364 ACC-TTTGCATGACT-C-TATCACAGAATGAGATAAATCAACACCGACATTTCCAGAG-AAAGTT
186 ACCTTTTGCATGACTCCATATC-CAGAAAGAGATAAAGCAACACAGACATTGCCAG-GTAAAGTT
*
1826425 CATAATGAGAAGAACTCATCT-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGC
249 CATAATGAGAAAAACTCATCTAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
*
1826488 TTG-ATTCTATCACAGAAAGAGATAGATCATCA
314 TCGAATTC-AT--C---AAGAGAT-G--CATCA
* *
1826520 TCAACTTTTCCA-AAAGAGTTCATAATGAGAAGAACTCATCCGAAGAAGGAGAATAAGTTCATAA
1 TCAACTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
*
1826584 TAAGAAGAACTTGTTCAACCTTTTGCTCG
66 TGAGAAGAACTTGTTCAACCTTTTGCTCG
1826613 GCTTTATCAC
Statistics
Matches: 368, Mismatches: 46, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
337 1 0.00
338 34 0.09
339 37 0.10
340 18 0.05
341 38 0.10
342 3 0.01
344 1 0.00
345 4 0.01
346 4 0.01
347 52 0.14
348 16 0.04
349 121 0.33
350 34 0.09
351 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.26
Consensus pattern (337 bp):
TCAACTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGATCCACGGATCAACATTGCCAGAGAAAGTTCATAAT
AAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTGGTTCAACCTTTTGCA
TGACTCCATATCCAGAAAGAGATAAAGCAACACAGACATTGCCAGGTAAAGTTCATAATGAGAAA
AACTCATCTAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCA
AGAGATGCATCA
Found at i:1826681 original size:238 final size:237
Alignment explanation
Indices: 1826299--1826744 Score: 630
Period size: 238 Copynumber: 1.9 Consensus size: 237
1826289 TGCCAGAGAA
* * *
1826299 AGTTCATAATAAGAAGAACTTATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTGGTTCA
1 AGTTCATAATAAGAAGAACTCATCCGAAGAGAAAGAAGAAGTTCATAATAAGAAGAACTGGTTCA
* *
1826364 ACCTTTGCATGACTCTATCACAGAATGAGATAAATCAACACCGACATTTCCAGAGAAAGTTCATA
66 ACCTTTGCATGACTCTATCACAGAAGGAGATAAATCAACACCAACATTTCCAGAGAAAGTTCATA
* * *
1826429 ATGAGAAGAACTCATCT-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTG-CTTGA
131 ATGAGAAAAACTCATCTAGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACC-TTGCCTTAA
1826492 TTCTATCACAGAAAGAGATAGATCATCATCAACTTTTCCAAAAG
195 TTC-ATCACAGAAAGAGATAGATCATCATCAACTTTTCCAAAAG
* * * *
1826536 AGTTCATAATGAGAAGAACTCATCCGAAGA-AGGAGAATAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATAAGAAGAACTCATCCGAAGAGA-AAGAAGAAGTTCATAATAAGAAGAACTGGTTC
* * * *
1826600 AACCTTTTGC-TCGGCTTTATCACAGAAGGAGATAGATCAGCACCAACATTTCCAGAGAAAGTTC
65 AACC-TTTGCAT-GACTCTATCACAGAAGGAGATAAATCAACACCAACATTTCCAGAGAAAGTTC
1826664 ATAATGAGAAAAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTT
128 ATAATGAGAAAAACTCATCT----A-GAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTT
1826729 GCCTTAATTCATCACA
188 GCCTTAATTCATCACA
1826745 TATGAAATTG
Statistics
Matches: 183, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
236 1 0.01
237 60 0.33
238 70 0.38
243 9 0.05
244 43 0.23
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (237 bp):
AGTTCATAATAAGAAGAACTCATCCGAAGAGAAAGAAGAAGTTCATAATAAGAAGAACTGGTTCA
ACCTTTGCATGACTCTATCACAGAAGGAGATAAATCAACACCAACATTTCCAGAGAAAGTTCATA
ATGAGAAAAACTCATCTAGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTGCCTTAAT
TCATCACAGAAAGAGATAGATCATCATCAACTTTTCCAAAAG
Found at i:1826892 original size:137 final size:137
Alignment explanation
Indices: 1826666--1826997 Score: 511
Period size: 137 Copynumber: 2.4 Consensus size: 137
1826656 GAAAGTTCAT
* * *
1826666 AATGAGAAAAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTGC
1 AATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTGC
* * *
1826731 CTTAATTCATCACATATGAAATTGAATCAACGATACCTCTTTTGAGGATTAGCATTTCTAGAAGG
66 CTTAATTCATCACATATGAAATTGAATCAACGACACCTCTTTTGAGGATCAGCATTTCCAGAAGG
* *
1826796 AGTTCGC
131 AGCTCAC
* * *
1826803 AATGAGAATAACTCATCTGAAGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTTC
1 AATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTGC
*
1826868 CTTAATTCATCATATATGAAATTGAATCAACGACACCTCTTTTGAGGATCAGCATTTCCAGAAGG
66 CTTAATTCATCACATATGAAATTGAATCAACGACACCTCTTTTGAGGATCAGCATTTCCAGAAGG
1826933 AGCTCAC
131 AGCTCAC
* * ** *
1826940 AATGAGAAGAACTCATCTGAAGAGGAAGCAGAAGTTCATAATCTGAAGAACTTATTCA
1 AATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1826998 GCCTTTTACT
Statistics
Matches: 177, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
137 177 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (137 bp):
AATGAGAAAAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAACTTGC
CTTAATTCATCACATATGAAATTGAATCAACGACACCTCTTTTGAGGATCAGCATTTCCAGAAGG
AGCTCAC
Found at i:1827567 original size:2 final size:2
Alignment explanation
Indices: 1827560--1827586 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1827550 TTATTATTAT
1827560 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1827587 TTAAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1831068 original size:18 final size:18
Alignment explanation
Indices: 1831035--1831069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1831025 AAATTCAAGG
**
1831035 CAACATGGGCGGCTAAAT
1 CAACATGGGCAACTAAAT
1831053 CAACATGGGCAACTAAA
1 CAACATGGGCAACTAAA
1831070 ATTGGTCCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (18 bp):
CAACATGGGCAACTAAAT
Found at i:1831941 original size:2 final size:2
Alignment explanation
Indices: 1831936--1831962 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1831926 AAACACACAC
1831936 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1831963 ATCTTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1832985 original size:14 final size:15
Alignment explanation
Indices: 1832957--1832985 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1832947 AAAAATAATA
1832957 TTTTAATTTTAATTT
1 TTTTAATTTTAATTT
1832972 TTTTAA-TTTAATTT
1 TTTTAATTTTAATTT
1832986 AATTTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTTTAATTT
Found at i:1833077 original size:11 final size:11
Alignment explanation
Indices: 1833061--1833087 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1833051 TCTATTTAAA
1833061 AATTTTAAATT
1 AATTTTAAATT
1833072 AATTTTAAATT
1 AATTTTAAATT
1833083 AATTT
1 AATTT
1833088 GTACAGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTAAATT
Found at i:1842097 original size:230 final size:229
Alignment explanation
Indices: 1841392--1842319 Score: 1149
Period size: 230 Copynumber: 4.0 Consensus size: 229
1841382 ATTATGCTCT
* * * *
1841392 TCATCTTGTATGTTCCTTGTTATTAATGTTCTTACGGATGGTCCTGTGCTGATTAGATTGTTCTC
1 TCATCTTTTATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
* * * *** * * *
1841457 TGTCAGCACATAACATATTCAGAAGTTACATTTTATGACCATGTTATGCATTTTTGTTCTCCTCT
66 CGTCAGCACATAACATATTCATAAGCTACACGCTATGGCCATATTATG-TTTTTTGTTCT-CT-T
* * *
1841522 CCACTGAATGAGGAAGACTATTTATTCTGT-GCAAATATTACATACCTATTTACCTTTATGTCTT
128 -CACTGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATACCTATTTATCTTTATGCCTT
* * * * * *
1841586 GCCGTTTTCATAGCAGTTTTGGTTAGTGCTCATTGATATGCTTACA
192 -CTGTTTCCATAGCAGTTCTGTTTGGTGGTCATTG--A----TA-A
* * *
1841632 CTCATCATCTTGAATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAAAATGT
1 -TCATC-T-TT-TATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGT
1841697 TCTCCGTCAGCACATAACATATTCATAAGCTACACGC-ATGGCCATATTATG-TTTTTGTTCTCT
62 TCTCCGTCAGCACATAACATATTCATAAGCTACACGCTATGGCCATATTATGTTTTTTGTTCTCT
* *
1841760 TCACTGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATATCTATTTATCTTTTTGCCTA
127 TCACTGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATACCTATTTATCTTTATGCCT-
1841825 TCTGTTTCCATAGCAGTTCTGTTTGGTGGTCATTGATAA
191 TCTGTTTCCATAGCAGTTCTGTTTGGTGGTCATTGATAA
*
1841864 TCATCTTTTATGTTCCTTGGTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
1 TCATCTTTTATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
**
1841929 CGTTGGCACATAACATATTCATAAGCTACACGCT-TGGCCATATTATGTTTTTATGTTCTCTTCA
66 CGTCAGCACATAACATATTCATAAGCTACACGCTATGGCCATATTATGTTTTT-TGTTCTCTTCA
* * *
1841993 TTGAATGAGGAAGACTGTTCATTCTGTGGCGAATATTACATACCTATTTATCTTTATGCCTATCT
130 CTGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATACCTATTTATCTTTATGCCT-TCT
1842058 GTTTCCAT-GACAGTTCTGTTTGGTGGTCATTGATAA
194 GTTTCCATAG-CAGTTCTGTTTGGTGGTCATTGATAA
*
1842094 TCATCTTTTATGTTCCTTGTTATTGATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
1 TCATCTTTTATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
* * * * * *
1842159 TGTCAGCACATAATATATTCATAAACTACATG-TATGCCCATATTATGTTTTTTGTTATCCTCTC
66 CGTCAGCACATAACATATTCATAAGCTACACGCTATGGCCATATTATGTTTTTTG-T-T-CTCTT
* * *
1842223 CACTGAATGAGGAAGACTATTCATTTTGTGGCAAAAATTACATACTTATTTTATC-TT-TG---T
128 CACTGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATACCTA-TTTATCTTTATGCCTT
* * *
1842283 CTGTTTCCATGGCAGTTTTGTTTGGTTGTCATTGATA
192 CTGTTTCCATAGCAGTTCTGTTTGGTGGTCATTGATA
1842320 TGCTTACACT
Statistics
Matches: 617, Mismatches: 55, Indels: 44
0.86 0.08 0.06
Matches are distributed among these distances:
227 34 0.06
228 98 0.16
229 10 0.02
230 213 0.35
231 8 0.01
232 49 0.08
233 8 0.01
237 1 0.00
238 28 0.05
239 58 0.09
240 3 0.00
241 15 0.02
242 1 0.00
243 13 0.02
244 78 0.13
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (229 bp):
TCATCTTTTATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
CGTCAGCACATAACATATTCATAAGCTACACGCTATGGCCATATTATGTTTTTTGTTCTCTTCAC
TGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATACCTATTTATCTTTATGCCTTCTGT
TTCCATAGCAGTTCTGTTTGGTGGTCATTGATAA
Found at i:1842202 original size:458 final size:467
Alignment explanation
Indices: 1841185--1842319 Score: 1227
Period size: 451 Copynumber: 2.5 Consensus size: 467
1841175 CCAGCCTCTT
* * * * * * ***
1841185 TCATCTTGTATTTTCCCTGTTAGTAATGTGCTTATGGACGTTCCTGCGCTGATTATGTTGTTCTC
1 TCATCTTGAATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAAAATGTTCTC
* * * * * *
1841250 CATCAGCACATAACATATTCATAAGCTACATGTATGGCCATATTATG-TTTTTGTTCT-CT-TCC
66 CGTCAGCACATAACATATTCATAAACTACACGCATGCCCATATTATGTTTTTTGTTATCCTCTCC
* * * *
1841312 -CTGAATGAGGGAGACTATTCATTCTGTGGTAAAAATTACATACCTA-TTTA-C----CCT-TAT
131 ACTGAATGAGGAAGACTATTCATTCTGTGGCAAAAATTACATACTTATTTTATCTTTGTCTGT-T
* * * ** * *
1841369 TCC-T--CTG-TCTG--TGAT--T-A-TGCTCTTCATCTTGTATGTTCCTTGTTATTAATGTTCT
195 TCCATAGCAGTTCTGTTTGGTGGTCATTGATAATCATCTTGTATGTTCCTTGGTATTAATGTGCT
* * * **
1841424 TACGGATGGTCCTGTGCTGATTAGATTGTTCTCTGTCAGCACATAACATATTCAGAAGTTACATT
260 TACGGACGGTCCTGTGCTGATTAGATTGTTCTCCGTCAGCACATAACATATTCAGAAGCTACACG
* * *
1841489 TTATGACCATGTTATGCATTTTTGTTCTCCTCTCCACTGAATGAGGAAGACTATTTATTCTGTGC
325 CTATGACCATATTATGCATTTTTGTTCTCCTCTCCACTGAATGAGGAAGACTATTCATTCTGTGC
* * *
1841554 AAATATTACATACCTATTTACCTTTATGTCTTGCCGTTTTCATAGCAGTTTTGGTTAGTGCTCAT
390 AAATATTACATACCTATTTACCTTTATGCCTTGCCGTTTCCATAGCAGTTCTGGTTAGTGCTCAT
1841619 TGATATGCTTACACTCA
455 TGA-A---TTACACTCA
1841636 TCATCTTGAATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAAAATGTTCTC
1 TCATCTTGAATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAAAATGTTCTC
* * *
1841701 CGTCAGCACATAACATATTCATAAGCTACACGCATGGCCATATTATG-TTTTTG-T-T-CTCTTC
66 CGTCAGCACATAACATATTCATAAACTACACGCATGCCCATATTATGTTTTTTGTTATCCTCTCC
*
1841762 ACTGAATGAGGAAGACTATTCATTCTGTGGCAAATATTACATA-TCTA-TTTATCTTTTTGCCTA
131 ACTGAATGAGGAAGACTATTCATTCTGTGGCAAAAATTACATACT-TATTTTATC--TTTG----
*
1841825 TCTGTTTCCATAGCAGTTCTGTTTGGTGGTCATTGATAATCATCTTTTATGTTCCTTGGTATTAA
189 TCTGTTTCCATAGCAGTTCTGTTTGGTGGTCATTGATAATCATCTTGTATGTTCCTTGGTATTAA
* ** *
1841890 TGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTCCGTTGGCACATAACATATTCATAAGC
254 TGTGCTTACGGACGGTCCTGTGCTGATTAGATTGTTCTCCGTCAGCACATAACATATTCAGAAGC
* * * *
1841955 TACACGCT-TGGCCATATTATG-TTTTTATGTTCT-CT-T-CATTGAATGAGGAAGACTGTTCAT
319 TACACGCTATGACCATATTATGCATTTT-TGTTCTCCTCTCCACTGAATGAGGAAGACTATTCAT
* * * *
1842015 TCTGTGGCGAATATTACATACCTATTTATCTTTATGCCTAT-CTGTTTCCAT-GACAGTTCTGTT
383 TCTGT-GCAAATATTACATACCTATTTACCTTTATGCCT-TGCCGTTTCCATAG-CAGTTCTGGT
* *
1842078 TGGTGGTCATTG-A-TA-A-TCA
445 TAGTGCTCATTGAATTACACTCA
* * * *
1842097 TC-T-TT-TATGTTCCTTGTTATTGATGTGCTTATGGACGGTCCTGTGCTGATTAGATTGTTCTC
1 TCATCTTGAATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAAAATGTTCTC
* * * *
1842159 TGTCAGCACATAATATATTCATAAACTACATGTATGCCCATATTATGTTTTTTGTTATCCTCTCC
66 CGTCAGCACATAACATATTCATAAACTACACGCATGCCCATATTATGTTTTTTGTTATCCTCTCC
*
1842224 ACTGAATGAGGAAGACTATTCATTTTGTGGCAAAAATTACATACTTATTTTATCTTTGTCTGTTT
131 ACTGAATGAGGAAGACTATTCATTCTGTGGCAAAAATTACATACTTATTTTATCTTTGTCTGTTT
* * *
1842289 CCATGGCAGTTTTGTTTGGTTGTCATTGATA
196 CCATAGCAGTTCTGTTTGGTGGTCATTGATA
1842320 TGCTTACACT
Statistics
Matches: 582, Mismatches: 67, Indels: 64
0.82 0.09 0.09
Matches are distributed among these distances:
449 3 0.01
450 3 0.01
451 151 0.26
452 1 0.00
457 35 0.06
458 94 0.16
459 8 0.01
460 2 0.00
461 10 0.02
462 55 0.09
463 11 0.02
465 2 0.00
466 4 0.01
467 1 0.00
468 30 0.05
469 57 0.10
470 8 0.01
471 18 0.03
472 89 0.15
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (467 bp):
TCATCTTGAATGTTCCTTGTTATTAATGTGCTTATGGACGGTCCTGTGCTGATTAAAATGTTCTC
CGTCAGCACATAACATATTCATAAACTACACGCATGCCCATATTATGTTTTTTGTTATCCTCTCC
ACTGAATGAGGAAGACTATTCATTCTGTGGCAAAAATTACATACTTATTTTATCTTTGTCTGTTT
CCATAGCAGTTCTGTTTGGTGGTCATTGATAATCATCTTGTATGTTCCTTGGTATTAATGTGCTT
ACGGACGGTCCTGTGCTGATTAGATTGTTCTCCGTCAGCACATAACATATTCAGAAGCTACACGC
TATGACCATATTATGCATTTTTGTTCTCCTCTCCACTGAATGAGGAAGACTATTCATTCTGTGCA
AATATTACATACCTATTTACCTTTATGCCTTGCCGTTTCCATAGCAGTTCTGGTTAGTGCTCATT
GAATTACACTCA
Found at i:1852518 original size:35 final size:36
Alignment explanation
Indices: 1852472--1852557 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
1852462 GTAACTCTTC
*
1852472 ATCTTTTCCATTCGAAGCTGCTTCC-TTTTTTTTCA
1 ATCTTTTCCATTCAAAGCTGCTTCCTTTTTTTTTCA
*
1852507 ATCTTTTCCATTCAAAGCTTCTTCCTTTTTTTTTCA
1 ATCTTTTCCATTCAAAGCTGCTTCCTTTTTTTTTCA
*
1852543 ATCTTTTCAATTCAA
1 ATCTTTTCCATTCAA
1852558 TTTCAATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 23 0.49
36 24 0.51
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (36 bp):
ATCTTTTCCATTCAAAGCTGCTTCCTTTTTTTTTCA
Found at i:1855161 original size:4 final size:4
Alignment explanation
Indices: 1855152--1855188 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
1855142 AAAACTCTTT
1855152 TATC TATC TATC TATC TATC TATC TATC TAT- TATC TA
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TA
1855189 CTGACACTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:1856515 original size:22 final size:21
Alignment explanation
Indices: 1856476--1856516 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1856466 AGTGAAAAAA
**
1856476 CCGGATCGATTTTTATCCGAT
1 CCGGATCGATTTAAATCCGAT
1856497 CCGGATCGGATTTAAATCCG
1 CCGGATC-GATTTAAATCCG
1856517 GTTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
CCGGATCGATTTAAATCCGAT
Found at i:1859484 original size:34 final size:34
Alignment explanation
Indices: 1859441--1859508 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1859431 ATATATACAT
1859441 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1859475 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1859509 AACAAAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (34 bp):
GATTACAAGAGATCAATTAGGCTACAATTAAGGA
Found at i:1865704 original size:81 final size:80
Alignment explanation
Indices: 1865591--1865833 Score: 371
Period size: 81 Copynumber: 3.0 Consensus size: 80
1865581 GCCCGAGGGA
* * *
1865591 AGCTAGAGAGTGATAATACAGGAAGCAAAAAGAAGGATGATAACT-CAGCAAGCAAAAAGAAGTT
1 AGCTAGAGTGTGATAATACAGCAAGCAAAAAGAAGGGTGATAA-TACA-CAAGCAAAAAGAAGTT
*
1865655 AAAGCCTGATTTGGCTG
64 AAAGTCTGATTTGGCTG
1865672 AGCTAGAGTGTGATAATACAGCAAGCAAAAAGAAGGGTGATAATACAACAAGCAAAAAGAAGTTA
1 AGCTAGAGTGTGATAATACAGCAAGCAAAAAGAAGGGTGATAATAC-ACAAGCAAAAAGAAGTTA
1865737 AAGTCTGATTTGGCTG
65 AAGTCTGATTTGGCTG
* * *
1865753 AGCTACAGTGCGATAATACAGCAAGCAAAAAGAAGGGTGATAATACAAAGAGCAAAAAGAAGTTA
1 AGCTAGAGTGTGATAATACAGCAAGCAAAAAGAAGGGTGATAATACACA-AGCAAAAAGAAGTTA
*
1865818 AAGTCTGATTTAGCTG
65 AAGTCTGATTTGGCTG
1865834 CGAATGGGAG
Statistics
Matches: 151, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
80 3 0.02
81 147 0.97
82 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.19
Consensus pattern (80 bp):
AGCTAGAGTGTGATAATACAGCAAGCAAAAAGAAGGGTGATAATACACAAGCAAAAAGAAGTTAA
AGTCTGATTTGGCTG
Found at i:1865723 original size:27 final size:27
Alignment explanation
Indices: 1865681--1865733 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1865671 GAGCTAGAGT
*
1865681 GTGATAATACAGCAAGCAAAAAGAAGG
1 GTGATAATACAACAAGCAAAAAGAAGG
1865708 GTGATAATACAACAAGCAAAAAGAAG
1 GTGATAATACAACAAGCAAAAAGAAG
1865734 TTAAAGTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.55, C:0.11, G:0.23, T:0.11
Consensus pattern (27 bp):
GTGATAATACAACAAGCAAAAAGAAGG
Found at i:1873288 original size:2 final size:2
Alignment explanation
Indices: 1873281--1873310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1873271 AATTTAATTC
1873281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1873311 TGATTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1875612 original size:48 final size:49
Alignment explanation
Indices: 1875534--1875668 Score: 184
Period size: 48 Copynumber: 2.8 Consensus size: 49
1875524 AAACAAGGGC
*
1875534 GGACCTCCATGGAGCCCGGGGTATCCCGGGCAACCCCTCATCCAGGGGT
1 GGACCTACATGGAGCCCGGGGTATCCCGGGCAACCCCTCATCCAGGGGT
* *
1875583 GGACCTACGTGGAG-CCGGGGTATCTCGGGCAACCCCTCATCCAGGGGT
1 GGACCTACATGGAGCCCGGGGTATCCCGGGCAACCCCTCATCCAGGGGT
* * * **
1875631 -GACCTCCATGGTGCCCGAGGTATCCCAAGCAACCCCTC
1 GGACCTACATGGAGCCCGGGGTATCCCGGGCAACCCCTC
1875669 CACAAGTGCC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
47 10 0.13
48 53 0.71
49 12 0.16
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (49 bp):
GGACCTACATGGAGCCCGGGGTATCCCGGGCAACCCCTCATCCAGGGGT
Found at i:1875694 original size:18 final size:18
Alignment explanation
Indices: 1875671--1875720 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1875661 AACCCCTCCA
* *
1875671 CAAGTGCCACCCTTAATC
1 CAAGTGTCACCCCTAATC
1875689 CAAGTGTCACCCCTAATC
1 CAAGTGTCACCCCTAATC
1875707 CAAGTGTCACCCCT
1 CAAGTGTCACCCCT
1875721 GAGGCTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (18 bp):
CAAGTGTCACCCCTAATC
Found at i:1886513 original size:20 final size:20
Alignment explanation
Indices: 1886488--1886527 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1886478 TGGTTAACCG
1886488 TATCGTCAAAAATAGTGATT
1 TATCGTCAAAAATAGTGATT
1886508 TATCGTCAAAAATAGTGATT
1 TATCGTCAAAAATAGTGATT
1886528 AATAATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
TATCGTCAAAAATAGTGATT
Found at i:1888478 original size:2 final size:2
Alignment explanation
Indices: 1888471--1888495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1888461 AAAATCAACA
1888471 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1888496 GTAATCCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1899075 original size:15 final size:15
Alignment explanation
Indices: 1899055--1899083 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1899045 TTTTTACAGG
1899055 TTACATTGTAACCTA
1 TTACATTGTAACCTA
1899070 TTACATTGTAACCT
1 TTACATTGTAACCT
1899084 CGTCTGGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (15 bp):
TTACATTGTAACCTA
Found at i:1902899 original size:179 final size:186
Alignment explanation
Indices: 1902617--1903509 Score: 814
Period size: 200 Copynumber: 4.6 Consensus size: 186
1902607 AATATATACA
* * * * * *
1902617 GTGTCGATACATTATGTAGACATATTTTCTCATAAAACTGGTAAATTTAAACCGGTTACATTGTA
1 GTGTCGATACTTTATGTATACATATTTTCTCATAAATC-GGTATATTTAGACCGGTTACATTGTT
* * * *
1902682 AAATGACATATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCG-AC---AT-T-T-TTTC
65 AATTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGAACTATATGTATCTTTC
*
1902740 GTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTT
130 GTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGATTT
* * * * *
1902797 GTGTCGACACTTTATGTATACTTGTTTTCTCATAAATCGGTGTATTTAGGCCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACATATTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTA
* * *
1902862 TTTTACCTATTACATTATAATTATGTGTTTTGATGTTTTTGGGATGGACACTTGTTATAAATGTA
66 ATTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGA-AC----TAT--ATGTA
1902927 TCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTG
124 T-----C--TTTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTG
1902992 GATTT
182 GATTT
*
1902997 GTGTCGATACTTTATGTATACATATTTTCTCAAAAATCGGTATATTTAGACCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACATATTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTA
* * * * * * *
1903062 GTTTATCTATTACATTATAATTATATGTTTCGATGATTTTAGTATCAACACTTGTTATAAATGTA
66 ATTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGA-AC----TAT--ATGTA
* * *
1903127 TCGACATATTGTCGTGCATTTTGTTTGGAAAATATATT-TGGACAAAAAGTATCGACACTTGTTG
124 T---C---TT-TCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTG
*
1903191 AATTT
182 GATTT
* * * * ** *
1903196 GTGTCGAAACTTTATGTATACATGTTTTCTCATAAACCGGTGTATTTAGGTCGGTTGCATTGTTA
1 GTGTCGATACTTTATGTATACATATTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTA
* * * * * * * *
1903261 TTTTACATATTACATTAT-ATCTTTGTGTTTCGATATTTTTAGTATTGACAATTGTTATAAATGT
66 ATTTACCTATTACATTATAAT-TATGTGTTTCGATGTTTTTGGGATCG--AA---CTAT--ATGT
* * *
1903325 ATCGACACTTTGTCGAGCACTTGGTTTGAAAAAATACATTATGGACAAAAAGTATCGACACTTGT
123 AT-----C-TT-TCGTGCACTTGGTTTG-GAAAATACATTCTGGACAAAAAGTATCGACACTTGT
*
1903390 TGAATTT
180 TGGATTT
* * *
1903397 GTGTTGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACATATTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTA
* * *
1903462 ATTTACCTATTACATTATAATTATTTGTTTCGATGATTTTGAGATCGA
66 ATTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGA
1903510 TACTTGTTAT
Statistics
Matches: 594, Mismatches: 85, Indels: 49
0.82 0.12 0.07
Matches are distributed among these distances:
179 62 0.10
180 32 0.05
181 2 0.00
190 2 0.00
191 1 0.00
192 1 0.00
198 4 0.01
199 153 0.26
200 210 0.35
201 125 0.21
202 2 0.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (186 bp):
GTGTCGATACTTTATGTATACATATTTTCTCATAAATCGGTATATTTAGACCGGTTACATTGTTA
ATTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGAACTATATGTATCTTTCG
TGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGATTT
Found at i:1903074 original size:200 final size:200
Alignment explanation
Indices: 1902726--1903572 Score: 1177
Period size: 200 Copynumber: 4.2 Consensus size: 200
1902716 TGTTTTTGGG
* *
1902726 ATCGACATTTTTTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTT
1 ATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTG-T
* * * * * * *
1902791 TG-ATTTGTGTCGACACTTTATGTATACTTGTTTTCTCATAAATCGGTGTATTTAGGCCGGTTAC
65 TGAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTAC
* * * *
1902855 ATTGTTATTTTACCTATTACATTATAATTATGTGTTTTGATGTTTTTGGGATGGACACTTGTTAT
130 ATTGTTATTTTACCTATTACATTATAATTATGTGTTTCGATGATTTTAGGATCGACACTTGTTAT
1902920 AAATGT
195 AAATGT
*
1902926 ATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTT
1 ATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
* *
1902991 GGATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAATCGGTATATTTAGACCGGTTACA
66 GAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTACA
* * * * *
1903056 TTGTTAGTTTATCTATTACATTATAATTATATGTTTCGATGATTTTAGTATCAACACTTGTTATA
131 TTGTTATTTTACCTATTACATTATAATTATGTGTTTCGATGATTTTAGGATCGACACTTGTTATA
1903121 AATGT
196 AATGT
* * * *
1903126 ATCGACA-TATTGTCGTGCATTTTGTTTGGAAAATATATT-TGGACAAAAAGTATCGACACTTGT
1 ATCGACACT-TTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGT
* * * * ** *
1903189 TGAATTTGTGTCGAAACTTTATGTATACATGTTTTCTCATAAACCGGTGTATTTAGGTCGGTTGC
65 TGAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTAC
* * * * *
1903254 ATTGTTATTTTACATATTACATTAT-ATCTTTGTGTTTCGAT-ATTTTTAGTATTGACAATTGTT
130 ATTGTTATTTTACCTATTACATTATAAT-TATGTGTTTCGATGA-TTTTAGGATCGACACTTGTT
1903317 ATAAATGT
193 ATAAATGT
* * *
1903325 ATCGACACTTTGTCGAGCACTTGGTTTGAAAAAATACATTATGGACAAAAAGTATCGACACTTGT
1 ATCGACACTTTTTCGTGCACTTGGTTTG-GAAAATACATTATGGACAAAAAGTATCGACACTTGT
*
1903390 TGAATTTGTGTTGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTAC
65 TGAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTAC
* * *
1903455 ATTGTTAATTTACCTATTACATTATAATTATTTGTTTCGATGATTTT-GAGATCGATACTTGTTA
130 ATTGTTATTTTACCTATTACATTATAATTATGTGTTTCGATGATTTTAG-GATCGACACTTGTTA
1903519 TAAATGT
194 TAAATGT
*
1903526 ATCGACACTTTTTTCGTGCACTTGGTTT-AAAAATACATTATGGACAA
1 ATCGACAC-TTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAA
1903573 CATGTATTGA
Statistics
Matches: 576, Mismatches: 60, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
198 3 0.01
199 165 0.29
200 243 0.42
201 145 0.25
202 20 0.03
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (200 bp):
ATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
GAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGGTTACA
TTGTTATTTTACCTATTACATTATAATTATGTGTTTCGATGATTTTAGGATCGACACTTGTTATA
AATGT
Found at i:1903474 original size:400 final size:400
Alignment explanation
Indices: 1902726--1903572 Score: 1326
Period size: 400 Copynumber: 2.1 Consensus size: 400
1902716 TGTTTTTGGG
*
1902726 ATCGACATTTTTTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACACTTGTT
1 ATCGACATTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
* * *
1902791 TGATTTGTGTCGACACTTTATGTATACTTGTTTTCTCATAAATCGGTGTATTTAGGCCGGTTACA
66 TGATTTGTGTCGAAACTTTATGTATACATGTTTTCTCATAAACCGGTGTATTTAGGCCGGTTACA
* * * * *
1902856 TTGTTATTTTACCTATTACATTATAATTATGTGTTTTGATGTTTTTGGGATGGACACTTGTTATA
131 TTGTTATTTTACATATTACATTATAATTATGTGTTTCGATATTTTTAGGATGGACAATTGTTATA
* * * *
1902921 AATGTATCGACACTTTTTCGTGCACTTGGTTTGGAAAATACATTCTGGACAAAAAGTATCGACAC
196 AATGTATCGACACTTTGTCGAGCACTTGGTTTGAAAAATACATTATGGACAAAAAGTATCGACAC
* *
1902986 TTGTTGGATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAATCGGTATATTTAGACCGG
261 TTGTTGAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGG
* *
1903051 TTACATTGTTAGTTTATCTATTACATTATAATTATATGTTTCGATGATTTT-AGTATCAACACTT
326 TTACATTGTTAATTTACCTATTACATTATAATTATATGTTTCGATGATTTTGAG-ATCAACACTT
1903115 GTTATAAATGT
390 GTTATAAATGT
* * * * *
1903126 ATCGACATATTGTCGTGCATTTTGTTTGGAAAATATATT-TGGACAAAAAGTATCGACACTTG-T
1 ATCGACATTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
* *
1903189 TGAATTTGTGTCGAAACTTTATGTATACATGTTTTCTCATAAACCGGTGTATTTAGGTCGGTTGC
66 TG-ATTTGTGTCGAAACTTTATGTATACATGTTTTCTCATAAACCGGTGTATTTAGGCCGGTTAC
* * *
1903254 ATTGTTATTTTACATATTACATTAT-ATCTTTGTGTTTCGATATTTTTAGTATTGACAATTGTTA
130 ATTGTTATTTTACATATTACATTATAAT-TATGTGTTTCGATATTTTTAGGATGGACAATTGTTA
1903318 TAAATGTATCGACACTTTGTCGAGCACTTGGTTTGAAAAAATACATTATGGACAAAAAGTATCGA
194 TAAATGTATCGACACTTTGTCGAGCACTTGGTTTG-AAAAATACATTATGGACAAAAAGTATCGA
*
1903383 CACTTGTTGAATTTGTGTTGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGAC
258 CACTTGTTGAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGAC
* * *
1903448 CGGTTACATTGTTAATTTACCTATTACATTATAATTATTTGTTTCGATGATTTTGAGATCGATAC
323 CGGTTACATTGTTAATTTACCTATTACATTATAATTATATGTTTCGATGATTTTGAGATCAACAC
1903513 TTGTTATAAATGT
388 TTGTTATAAATGT
*
1903526 ATCGACACTTTTTTCGTGCACTTGGTTT-AAAAATACATTATGGACAA
1 ATCGACA-TTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAA
1903573 CATGTATTGA
Statistics
Matches: 405, Mismatches: 36, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
398 5 0.01
399 166 0.41
400 209 0.52
401 25 0.06
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (400 bp):
ATCGACATTTTTTCGTGCACTTGGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTT
TGATTTGTGTCGAAACTTTATGTATACATGTTTTCTCATAAACCGGTGTATTTAGGCCGGTTACA
TTGTTATTTTACATATTACATTATAATTATGTGTTTCGATATTTTTAGGATGGACAATTGTTATA
AATGTATCGACACTTTGTCGAGCACTTGGTTTGAAAAATACATTATGGACAAAAAGTATCGACAC
TTGTTGAATTTGTGTCGATACTTTATGTATACATATTTTCTCAAAAACCGGTATATTTAGACCGG
TTACATTGTTAATTTACCTATTACATTATAATTATATGTTTCGATGATTTTGAGATCAACACTTG
TTATAAATGT
Found at i:1903820 original size:24 final size:24
Alignment explanation
Indices: 1903769--1903820 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1903759 ATTTACATTT
* *
1903769 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAAATG
*
1903793 AAATTCAAACTCTAATT-ATAAATG
1 AAATTCAAACTCAAATTGA-AAATG
1903817 AAAT
1 AAAT
1903821 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAAATG
Found at i:1905853 original size:39 final size:38
Alignment explanation
Indices: 1905810--1905942 Score: 110
Period size: 39 Copynumber: 3.4 Consensus size: 38
1905800 AAAATATCAT
*
1905810 TTTTCTACCTATAATATTATATACAAGTATCCATATTTA
1 TTTTCTACCTAGAATATTATATACAAGTAT-CATATTTA
* * * *
1905849 TTTTCTACCTAGAATATCACTTTCTACATGTA--ATA-TCA
1 TTTTCTACCTAGAATAT---TATATACAAGTATCATATTTA
* * * *
1905887 TTTTTTACCTATAATATTAAATAAAAGTATCGATATTTA
1 TTTTCTACCTAGAATATTATATACAAGTATC-ATATTTA
*
1905926 TTATCTACCTAGAATAT
1 TTTTCTACCTAGAATAT
1905943 CACTTTCTAC
Statistics
Matches: 71, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
35 7 0.10
38 20 0.28
39 35 0.49
42 9 0.13
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (38 bp):
TTTTCTACCTAGAATATTATATACAAGTATCATATTTA
Found at i:1905874 original size:19 final size:19
Alignment explanation
Indices: 1905850--1905903 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1905840 CCATATTTAT
1905850 TTTCTACCTAGAATATCAC
1 TTTCTACCTAGAATATCAC
* *
1905869 TTTCTACAT-GTAATATCAT
1 TTTCTACCTAG-AATATCAC
* *
1905888 TTTTTACCTATAATAT
1 TTTCTACCTAGAATAT
1905904 TAAATAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (19 bp):
TTTCTACCTAGAATATCAC
Found at i:1905933 original size:77 final size:78
Alignment explanation
Indices: 1905802--1905959 Score: 273
Period size: 77 Copynumber: 2.0 Consensus size: 78
1905792 TACAACCTAA
* * *
1905802 AATATCATTTTTCTACCTATAATATTATATACAAGTATCCATATTTATTTTCTACCTAGAATATC
1 AATATCATTTTTCTACCTATAATATTAAATAAAAGTATCCATATTTATTATCTACCTAGAATATC
1905867 ACTTTCTACATGT
66 ACTTTCTACATGT
*
1905880 AATATCATTTTT-TACCTATAATATTAAATAAAAGTATCGATATTTATTATCTACCTAGAATATC
1 AATATCATTTTTCTACCTATAATATTAAATAAAAGTATCCATATTTATTATCTACCTAGAATATC
1905944 ACTTTCTACATGT
66 ACTTTCTACATGT
1905957 AAT
1 AAT
1905960 CGATCCCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 64 0.84
78 12 0.16
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (78 bp):
AATATCATTTTTCTACCTATAATATTAAATAAAAGTATCCATATTTATTATCTACCTAGAATATC
ACTTTCTACATGT
Found at i:1906529 original size:161 final size:160
Alignment explanation
Indices: 1906324--1906659 Score: 516
Period size: 161 Copynumber: 2.1 Consensus size: 160
1906314 TTTGAGACCG
* * *
1906324 GTTTTGTCATATTTTTA-TCTGTTATATTATTATGGATCGATACATTTTTTAAAGTATCGAGATT
1 GTTTTGTCATATTTTTACT-TGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACT
* *
1906388 TTATAGGCGCTATATCTTATTATCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
65 TTATAGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCG
1906453 ACACTTTCAACATATCCGATATTTTTTTACAT
130 ACACTTTCAACATATCCGATATTTTTTTAC-T
* *
1906485 GTTTTGTCATATTTTTACTTTTTATATTGTTATGGATCGATACATTTTTTAAAGTATCAACACTT
1 GTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTT
* *
1906550 TATACGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCAA
66 TATAGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCGA
* *
1906615 CACTTTCAACATAT-CTAGTATCTTTTTACCT
131 CACTTTCAACATATCCGA-TATTTTTTTA-CT
1906646 GTTTTGTCAT-TTTT
1 GTTTTGTCATATTTT
1906660 GAGACATGTT
Statistics
Matches: 161, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
160 6 0.04
161 153 0.95
162 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (160 bp):
GTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTT
TATAGGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCCGATATTTTTTTACT
Found at i:1906788 original size:183 final size:182
Alignment explanation
Indices: 1906485--1907079 Score: 846
Period size: 182 Copynumber: 3.3 Consensus size: 182
1906475 TTTTTTACAT
* *
1906485 GTTTTGTCATATTTTTACTTTTTATATTGTTATGGATCGATACA-TTTTTTAAAGTATCAACACT
1 GTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* * *
1906549 TTATACGCGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCA
66 TTATAAGCGCTATAACTTATTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAATTATCG
*
1906614 ACACTTTCAACATATCTAGTATCTTTTTACCTG-TTTTGTCATTTTTGAGACAT
131 ACACTTTCAACATATCTAGTATC-TTTTACCTGATTTTGTCA-TTTTGAGACAG
* *
1906667 GTTTTGTTATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTTGAAGTATCGACACT
1 GTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* *
1906732 TTATAGGCGCTATAACTTATTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAAGTATCG
66 TTATAAGCGCTATAACTTATTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAATTATCG
1906797 ACACTTTCAACATATCCGATAGT-TC-TTTA-CTGATTTTGTCATTTTGAGATC-G
131 ACACTTTCAACATAT-C--TAGTATCTTTTACCTGATTTTGTCATTTTGAGA-CAG
* **
1906849 GTTTTGTCATATTTTTAAC-TGTTATATTGTTATGGATCGATATATTTTCATAAAGTATCGACAC
1 GTTTTGTCATATTTTT-ACTTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
* *
1906913 TTTTTAAGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
65 TTTATAAGCGCTATAACTTATTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAATTATC
** * * *
1906978 GACACTTTCAACATATCCGGTAGCGTTTTACC-GATTTTGTCATTTCGAGACCG
130 GACACTTTCAACATATCTAGTATC-TTTTACCTGATTTTGTCATTTTGAGACAG
* * * *
1907031 GTTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATACATTTTT
1 GTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTT
1907080 CATTCGTATC
Statistics
Matches: 373, Mismatches: 27, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
179 2 0.01
180 1 0.00
181 4 0.01
182 249 0.67
183 110 0.29
184 1 0.00
185 2 0.01
186 4 0.01
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
GTTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
TTATAAGCGCTATAACTTATTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAAATTATCG
ACACTTTCAACATATCTAGTATCTTTTACCTGATTTTGTCATTTTGAGACAG
Found at i:1907936 original size:36 final size:36
Alignment explanation
Indices: 1907896--1907971 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
1907886 ATTAATATCG
1907896 TGAACTTTGCAGCTGTTTTCAATTTAATTTTAAATT
1 TGAACTTTGCAGCTGTTTTCAATTTAATTTTAAATT
1907932 TGAACTTTGCAGCTGTTTTCAATTTAATTTTAAATT
1 TGAACTTTGCAGCTGTTTTCAATTTAATTTTAAATT
1907968 TGAA
1 TGAA
1907972 TTAATTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (36 bp):
TGAACTTTGCAGCTGTTTTCAATTTAATTTTAAATT
Found at i:1914642 original size:25 final size:24
Alignment explanation
Indices: 1914606--1914656 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1914596 GCATTGCTCC
1914606 CCCGTCCTCGTCCCCGTTTAAAAAA
1 CCCGTCCTCGT-CCCGTTTAAAAAA
1914631 CCCGTACC-CGTCCCGTTTAAAAAA
1 CCCGT-CCTCGTCCCGTTTAAAAAA
1914655 CC
1 CC
1914657 GCGGTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 15 0.60
25 8 0.32
26 2 0.08
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (24 bp):
CCCGTCCTCGTCCCGTTTAAAAAA
Found at i:1921618 original size:32 final size:32
Alignment explanation
Indices: 1921582--1921645 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1921572 TTAATTAATG
* *
1921582 ATATTAATAAAATTTATGAAGCTGAAAATATA
1 ATATTAATAAAATTTATAAAGCTCAAAATATA
*
1921614 ATATTAATAAAATTTATAAAGTTCAAAATATA
1 ATATTAATAAAATTTATAAAGCTCAAAATATA
1921646 TGATTATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (32 bp):
ATATTAATAAAATTTATAAAGCTCAAAATATA
Found at i:1933421 original size:21 final size:19
Alignment explanation
Indices: 1933396--1933456 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 19
1933386 ACAAGCTTAC
1933396 AATAAGTATTAAATGGTAAAT
1 AATAA-TATTAAAT-GTAAAT
1933417 AATAATA--AAAT-TACAAT
1 AATAATATTAAATGTA-AAT
1933434 AACTAATATTAAATGATAAAT
1 AA-TAATATTAAATG-TAAAT
1933455 AA
1 AA
1933457 ATTAACTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 9 0.26
20 6 0.18
21 10 0.29
22 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (19 bp):
AATAATATTAAATGTAAAT
Found at i:1933463 original size:26 final size:25
Alignment explanation
Indices: 1933433--1933482 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1933423 AAAATTACAA
1933433 TAACTAATATTAAATGATAAATAAAT
1 TAACTAATATTAAATGAT-AATAAAT
* *
1933459 TAACTGATATTAAATGGTAATAAA
1 TAACTAATATTAAATGATAATAAA
1933483 CAAAATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (25 bp):
TAACTAATATTAAATGATAATAAAT
Found at i:1934413 original size:9 final size:8
Alignment explanation
Indices: 1934379--1934425 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1934369 ATATCTGCAA
*
1934379 AAATAAAT
1 AAATAATT
*
1934387 AAATAAAT
1 AAATAATT
1934395 AAA-ATATT
1 AAATA-ATT
1934403 AAATAATTT
1 AAATAA-TT
1934412 AAATAATT
1 AAATAATT
1934420 AAATAA
1 AAATAA
1934426 AATAATAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
7 1 0.03
8 25 0.71
9 9 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAATAATT
Found at i:1934415 original size:29 final size:31
Alignment explanation
Indices: 1934382--1934454 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
1934372 TCTGCAAAAA
* *
1934382 TAAATAAATAAATAAAATATTAA-ATAAT-T
1 TAAATAAATAAATAAAATAATAACAAAATAT
*
1934411 TAAATAATTAAATAAAATAATAACAAAATAT
1 TAAATAAATAAATAAAATAATAACAAAATAT
1934442 TAAATATAATAAA
1 TAAATA-AATAAA
1934455 ATATACCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.57
30 4 0.11
31 7 0.19
32 5 0.14
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (31 bp):
TAAATAAATAAATAAAATAATAACAAAATAT
Found at i:1934455 original size:17 final size:18
Alignment explanation
Indices: 1934382--1934458 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 18
1934372 TCTGCAAAAA
1934382 TAAATAAATAAATAAAATAT
1 TAAAT-AAT-AATAAAATAT
1934402 TAAATAATTTAAATAATTAA-AT
1 TAAATAA--T-AATAA--AATAT
* *
1934424 AAAATAATAACAAAATAT
1 TAAATAATAATAAAATAT
1934442 TAAAT-ATAATAAAATAT
1 TAAATAATAATAAAATAT
1934459 ACCTTAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
17 13 0.27
18 6 0.12
19 6 0.12
20 6 0.12
21 7 0.15
22 8 0.17
23 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAATAATAATAAAATAT
Found at i:1934996 original size:20 final size:22
Alignment explanation
Indices: 1934951--1935011 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1934941 ATGAATATCA
1934951 ATATTTAAAAAATAATTTATAT
1 ATATTTAAAAAATAATTTATAT
1934973 ATATTTAAATAAAT-A-TTA-AT
1 ATATTTAAA-AAATAATTTATAT
*
1934993 ATA-TT-AAAAATGATTTATA
1 ATATTTAAAAAATAATTTATA
1935012 CCGATTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 4 0.11
18 3 0.09
19 5 0.14
20 6 0.17
21 3 0.09
22 10 0.29
23 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTTAAAAAATAATTTATAT
Found at i:1935215 original size:18 final size:17
Alignment explanation
Indices: 1935188--1935227 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1935178 TTAGTAAACT
1935188 AAAA-AATAGAAGAAGAA
1 AAAACAATAGAAGAA-AA
*
1935205 AAAACAATAGAGGAAAA
1 AAAACAATAGAAGAAAA
1935222 AAAACA
1 AAAACA
1935228 CTAAAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.75, C:0.05, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAACAATAGAAGAAAA
Found at i:1940441 original size:28 final size:28
Alignment explanation
Indices: 1940409--1940484 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 28
1940399 TTATATGACT
* **
1940409 ATATAATAATAATAAAAATAATATTTAA
1 ATATAATAATAATAAAAATAAAACATAA
* *
1940437 ATAT-ATAAACAAGTAAAATTAAAACATAA
1 ATATAAT-AATAA-TAAAAATAAAACATAA
*
1940466 ATA-AACAATAATAAAAATA
1 ATATAATAATAATAAAAATA
1940485 CAATTAGAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 16 0.43
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
ATATAATAATAATAAAAATAAAACATAA
Found at i:1941834 original size:3 final size:3
Alignment explanation
Indices: 1941828--1941942 Score: 144
Period size: 3 Copynumber: 38.0 Consensus size: 3
1941818 ATTATTTTTT
*
1941828 TAA TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1941873 TAA T-A TATA TATA TAA TAA TAA TAA TTA TTA TAA TAA TAA TTA TTA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1941919 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1941943 ATAAATAAGT
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.04
3 88 0.86
4 10 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1942487 original size:36 final size:36
Alignment explanation
Indices: 1942447--1942523 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
1942437 AGCAAAAAGT
*
1942447 TGAACAAGTTCTTCTTCAGATGAGTTCTTCTCATTA
1 TGAACAACTTCTTCTTCAGATGAGTTCTTCTCATTA
**
1942483 TGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
1 TGAACAACTTCTTCTTCAGATGAGTTCTTCTCATTA
1942519 TGAAC
1 TGAAC
1942524 TTTACCTGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (36 bp):
TGAACAACTTCTTCTTCAGATGAGTTCTTCTCATTA
Found at i:1942519 original size:237 final size:240
Alignment explanation
Indices: 1942229--1942699 Score: 752
Period size: 237 Copynumber: 2.0 Consensus size: 240
1942219 AGATTGAACA
1942229 AGTTATTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTT-CTC
1 AGTTATTCTCATTATGAACTTCTTCTT-CTCTTCAGATAAGTTCTTCTCATTATGAACTTTAC-C
* * *
1942293 TGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGA
64 TGGAAATATTGATCCATCAAGTGATGAATTTGAACAAAAAGTTAAACAAGTTCTTCTCATTATAA
* * **
1942358 ACTTCCTCTTCCTTCTTCAGATGAGTTCTACTCATTATGAACTC-TTCTGGAAATGCTGATCCAT
129 ACTTCCTCTTCATTCTTCAGATGAATTCTACTCATTATGAACTCGACCTGGAAATGCTGATCCAT
*
1942422 CGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTTCAGATG
194 CGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTATTCTTCAGATG
* *
1942469 AGTTCTTCTCATTATGAACTTCTTC-T-TCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTG
1 AGTTATTCTCATTATGAACTTCTTCTTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTACCTG
* *
1942532 GAAATATTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTCATTATAAAC
66 GAAATATTGATCCATCAAGTGATGAATTTGAACAAAAAGTTAAACAAGTTCTTCTCATTATAAAC
* * *
1942597 TTCTTCTTCATTCTTCAGATGAATTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCG
131 TTCCTCTTCATTCTTCAGATGAATTCTACTCATTATGAACTCGACCTGGAAATGCTGATCCATCG
*
1942662 AATGATGAATTCAAGCGAAAAGTTGAACAAGTTATTCT
196 AATGATGAATTCAAGCAAAAAGTTGAACAAGTTATTCT
1942700 CATTATGAAC
Statistics
Matches: 213, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
237 132 0.62
238 56 0.26
239 1 0.00
240 24 0.11
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (240 bp):
AGTTATTCTCATTATGAACTTCTTCTTCTCTTCAGATAAGTTCTTCTCATTATGAACTTTACCTG
GAAATATTGATCCATCAAGTGATGAATTTGAACAAAAAGTTAAACAAGTTCTTCTCATTATAAAC
TTCCTCTTCATTCTTCAGATGAATTCTACTCATTATGAACTCGACCTGGAAATGCTGATCCATCG
AATGATGAATTCAAGCAAAAAGTTGAACAAGTTATTCTTCAGATG
Found at i:1942521 original size:16 final size:17
Alignment explanation
Indices: 1942453--1942521 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
1942443 AAGTTGAACA
*
1942453 AGTTCTTCTTCA-GATG
1 AGTTCTTCTTCATTATG
1942469 AGTTCTTC-TCATTATG
1 AGTTCTTCTTCATTATG
*
1942485 AACTTCTTCTTC-TTCAGATG
1 -AGTTCTTCTTCATT---ATG
1942505 AGTTCTTC-TCATTATG
1 AGTTCTTCTTCATTATG
1942521 A
1 A
1942522 ACTTTACCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
15 3 0.07
16 15 0.35
17 9 0.21
18 4 0.09
19 9 0.21
20 3 0.07
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (17 bp):
AGTTCTTCTTCATTATG
Found at i:1942524 original size:36 final size:36
Alignment explanation
Indices: 1942455--1942525 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
1942445 GTTGAACAAG
1942455 TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1 TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1942491 TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1942526 TACCTGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (36 bp):
TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
Found at i:1942575 original size:125 final size:127
Alignment explanation
Indices: 1942341--1942586 Score: 360
Period size: 125 Copynumber: 1.9 Consensus size: 127
1942331 AGGTTAAACA
1942341 AGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTACTCATTATGAACTCTTCT
1 AGTTCTTCTCATTATGAACTT-CTCTTCCTTCTTCAGATGAGTTCTACTCATTATGAACTCTTCT
*
1942406 GGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTTCAGATG
65 GGAAATACTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTTCAGATG
*
1942469 AGTTCTTCTCATTATGAAC-T-TCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTACC
1 AGTTCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTACTCATTATGAACTCTT--C
* * *
1942530 TGGAAATATTGATCCATC-AAGTGATGGATTTGAA-CAAAAAGTTGAACAAGTTCTTCT
64 TGGAAATACTGATCCATCGAA-TGAT-GAATTCAAGCAAAAAGTTGAACAAGTTCTTCT
1942587 CATTATAAAC
Statistics
Matches: 109, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
123 2 0.02
124 33 0.30
125 48 0.44
126 6 0.06
127 1 0.01
128 19 0.17
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (127 bp):
AGTTCTTCTCATTATGAACTTCTCTTCCTTCTTCAGATGAGTTCTACTCATTATGAACTCTTCTG
GAAATACTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTTCAGATG
Found at i:1942631 original size:113 final size:110
Alignment explanation
Indices: 1942469--1942789 Score: 443
Period size: 113 Copynumber: 2.9 Consensus size: 110
1942459 TCTTCAGATG
**
1942469 AGTTCTTCTCATTATGAA---CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCT
*
1942531 GGAAATATTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
66 GG-AATGTTGATCCATCAA-TGATGGATTTGAACAAAAAGTTGAACA
* *
1942578 AGTTCTTCTCATTATAAACTTCTTCTTCATTCTTCAGATGAATTCTTCTCATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
* * * *
1942643 TGGTAATGCTGATCCATCGAATGAT-GAATTCAAGCGAAAAGTTGAACA
65 TGG-AATGTTGATCCATC-AATGATGGATTTGAA-CAAAAAGTTGAACA
*
1942691 AGTTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
1 AGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACC
*
1942756 TGGAATGTTGATCCATTGAATGATGGATTTGAAC
65 TGGAATGTTGATCCA-TCAATGATGGATTTGAAC
1942790 TTTGCTAAAA
Statistics
Matches: 186, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
109 17 0.09
112 31 0.17
113 135 0.73
114 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (110 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCT
GGAATGTTGATCCATCAATGATGGATTTGAACAAAAAGTTGAACA
Found at i:1943718 original size:114 final size:114
Alignment explanation
Indices: 1943471--1943920 Score: 733
Period size: 114 Copynumber: 4.0 Consensus size: 114
1943461 GATCATGCAG
* * * * * *** * *
1943471 TTCATCTTTTAATTCCAATGATTGGTTTTGTGGTTCCTATTGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
1943536 AAACTT-CAGAAGATGCTATTGGGTCTT-TTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
*
1943583 TTCATCTTTCAAATCCAATGATTGATTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1943648 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
*
1943697 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACTAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1943762 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
1943811 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
1943876 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAG
1943921 AACGTATCAC
Statistics
Matches: 317, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
112 59 0.19
113 21 0.07
114 237 0.75
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
Found at i:1944235 original size:19 final size:18
Alignment explanation
Indices: 1944211--1944259 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
1944201 AAAATAAAAG
1944211 AATAAATTGAATTTTTGAA
1 AATAAATTGAATTTTT-AA
*
1944230 AATAAATTGAA--TTTCA
1 AATAAATTGAATTTTTAA
1944246 AATAAATTGAATTT
1 AATAAATTGAATTT
1944260 AGAGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 1 0.04
19 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (18 bp):
AATAAATTGAATTTTTAA
Found at i:1952911 original size:66 final size:69
Alignment explanation
Indices: 1952818--1952970 Score: 188
Period size: 67 Copynumber: 2.2 Consensus size: 69
1952808 ACCATTTCAA
* *
1952818 GGGGAACCGATACCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCG-G-TACCCCC
1 GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGAGATA-CCCC
1952880 AGGGG
65 AGGGG
* * * *
1952885 GGGGAA-CGATACCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATCGATACCC
1 GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGA--GATACCC
1952949 CAGGGG
64 CAGGGG
*
1952955 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
1952971 CATGAGAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
66 18 0.25
67 29 0.40
70 16 0.22
71 10 0.14
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (69 bp):
GGGGAACCGATACCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGAGATACCCCA
GGGG
Found at i:1953596 original size:22 final size:22
Alignment explanation
Indices: 1953570--1953615 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1953560 GGACATAATT
1953570 CGGGCACTTCGGTGCAATTCTA
1 CGGGCACTTCGGTGCAATTCTA
1953592 CGGGCACTTCGGTGCAATTCTA
1 CGGGCACTTCGGTGCAATTCTA
1953614 CG
1 CG
1953616 AGAGGGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.26
Consensus pattern (22 bp):
CGGGCACTTCGGTGCAATTCTA
Found at i:1953800 original size:22 final size:22
Alignment explanation
Indices: 1953746--1953809 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
1953736 TTATGGACAT
1953746 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1953768 AA-T-T-CGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1953787 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1953809 A
1 A
1953810 TTTATACGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
19 17 0.44
20 2 0.05
21 2 0.05
22 18 0.46
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1953817 original size:22 final size:21
Alignment explanation
Indices: 1953751--1953817 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
1953741 GACATAATTC
1953751 TACGGGCACTTCGGTGCA--A
1 TACGGGCACTTCGGTGCATTA
* *
1953770 TTCGGGCACTTCGGTGCAATTC
1 TACGGGCACTTCGGTGC-ATTA
1953792 TACGGGCACTTCGGTGCATTTA
1 TACGGGCACTTCGGTGCA-TTA
1953814 TACG
1 TACG
1953818 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.40
20 1 0.03
21 1 0.03
22 22 0.55
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (21 bp):
TACGGGCACTTCGGTGCATTA
Found at i:1959889 original size:66 final size:63
Alignment explanation
Indices: 1959764--1959908 Score: 184
Period size: 66 Copynumber: 2.3 Consensus size: 63
1959754 ACCCATTCAA
* * *
1959764 GGGAACCGATACCCCTTCAACGAATGATTTCCAGAATGCTAGAGGGGAATCGGTACCCCAGGG
1 GGGAACCGATACCCCCTCAACGAATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGGG
* * *
1959827 GGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGA-GGGAATCGATACCCCCAG
1 GGGAACCGATACCCCCTCAACG-A-ATG-AATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAG
1959891 GG
62 GG
*
1959893 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
1959909 ATGAGAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
63 20 0.28
64 1 0.01
65 13 0.18
66 37 0.52
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.19
Consensus pattern (63 bp):
GGGAACCGATACCCCCTCAACGAATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGGG
Found at i:1960539 original size:22 final size:22
Alignment explanation
Indices: 1960511--1960555 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1960501 TTATGGACAT
1960511 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1960533 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1960555 A
1 A
1960556 TTTATACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1960563 original size:22 final size:22
Alignment explanation
Indices: 1960511--1960563 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1960501 TTATGGACAT
*
1960511 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
1960533 AATTCTACGGGCACTTCGGTGC
1 AATTATACGGGCACTTCGGTGC
*
1960555 ATTTATACG
1 AATTATACG
1960564 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (22 bp):
AATTATACGGGCACTTCGGTGC
Done.